<?xml version="1.0" encoding="us-ascii" standalone="yes"?>
<!-- DFIN ActiveDisclosure(SM) XBRL Linkbase Document - http://www.dfinsolutions.com/ -->
<!-- Creation Date      : 2021-05-11T16:27:29.7455687+00:00 -->
<!-- Version            : 5.0.1.615 -->
<!-- Package ID         : d28dd7db52004aa48bbd408a269d725d -->
<!-- Copyright (c) 2021 Donnelley Financial Solutions, Inc. All Rights Reserved. -->
<link:linkbase xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <link:roleRef roleURI="http://www.syndax.com/20210331/role/TemplateLink" xlink:href="sndx-20210331.xsd#TemplateLink" xlink:type="simple" />
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DocumentDocumentAndEntityInformation" xlink:href="sndx-20210331.xsd#Role_DocumentDocumentAndEntityInformation" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DocumentDocumentAndEntityInformation">
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_DocumentTransitionReport" xlink:type="locator" xlink:label="dei_DocumentTransitionReport" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_DocumentQuarterlyReport" xlink:type="locator" xlink:label="dei_DocumentQuarterlyReport" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_LocalPhoneNumber" xlink:type="locator" xlink:label="dei_LocalPhoneNumber" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_CityAreaCode" xlink:type="locator" xlink:label="dei_CityAreaCode" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityAddressPostalZipCode" xlink:type="locator" xlink:label="dei_EntityAddressPostalZipCode" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityAddressStateOrProvince" xlink:type="locator" xlink:label="dei_EntityAddressStateOrProvince" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityAddressCityOrTown" xlink:type="locator" xlink:label="dei_EntityAddressCityOrTown" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityAddressAddressLine3" xlink:type="locator" xlink:label="dei_EntityAddressAddressLine3" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityAddressAddressLine2" xlink:type="locator" xlink:label="dei_EntityAddressAddressLine2" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityAddressAddressLine1" xlink:type="locator" xlink:label="dei_EntityAddressAddressLine1" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityTaxIdentificationNumber" xlink:type="locator" xlink:label="dei_EntityTaxIdentificationNumber" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityIncorporationStateCountryCode" xlink:type="locator" xlink:label="dei_EntityIncorporationStateCountryCode" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityFileNumber" xlink:type="locator" xlink:label="dei_EntityFileNumber" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_SecurityExchangeName" xlink:type="locator" xlink:label="dei_SecurityExchangeName" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_Security12bTitle" xlink:type="locator" xlink:label="dei_Security12bTitle" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityShellCompany" xlink:type="locator" xlink:label="dei_EntityShellCompany" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityCommonStockSharesOutstanding" xlink:type="locator" xlink:label="dei_EntityCommonStockSharesOutstanding" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityExTransitionPeriod" xlink:type="locator" xlink:label="dei_EntityExTransitionPeriod" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityEmergingGrowthCompany" xlink:type="locator" xlink:label="dei_EntityEmergingGrowthCompany" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntitySmallBusiness" xlink:type="locator" xlink:label="dei_EntitySmallBusiness" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityFilerCategory" xlink:type="locator" xlink:label="dei_EntityFilerCategory" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_CurrentFiscalYearEndDate" xlink:type="locator" xlink:label="dei_CurrentFiscalYearEndDate" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityInteractiveDataCurrent" xlink:type="locator" xlink:label="dei_EntityInteractiveDataCurrent" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityCurrentReportingStatus" xlink:type="locator" xlink:label="dei_EntityCurrentReportingStatus" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityCentralIndexKey" xlink:type="locator" xlink:label="dei_EntityCentralIndexKey" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityRegistrantName" xlink:type="locator" xlink:label="dei_EntityRegistrantName" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_TradingSymbol" xlink:type="locator" xlink:label="dei_TradingSymbol" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_DocumentFiscalPeriodFocus" xlink:type="locator" xlink:label="dei_DocumentFiscalPeriodFocus" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_DocumentFiscalYearFocus" xlink:type="locator" xlink:label="dei_DocumentFiscalYearFocus" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_DocumentPeriodEndDate" xlink:type="locator" xlink:label="dei_DocumentPeriodEndDate" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_AmendmentFlag" xlink:type="locator" xlink:label="dei_AmendmentFlag" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_DocumentType" xlink:type="locator" xlink:label="dei_DocumentType" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_CoverAbstract" xlink:type="locator" xlink:label="dei_CoverAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_DocumentType" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_AmendmentFlag" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_DocumentPeriodEndDate" order="10050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_DocumentFiscalYearFocus" order="10070.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_DocumentFiscalPeriodFocus" order="10090.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_TradingSymbol" order="10110.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntityRegistrantName" order="10130.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntityCentralIndexKey" order="10150.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntityCurrentReportingStatus" order="10170.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntityInteractiveDataCurrent" order="10190.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_CurrentFiscalYearEndDate" order="10210.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntityFilerCategory" order="10230.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntitySmallBusiness" order="10250.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntityEmergingGrowthCompany" order="10270.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntityExTransitionPeriod" order="10290.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntityCommonStockSharesOutstanding" order="10310.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntityShellCompany" order="10330.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_Security12bTitle" order="10350.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_SecurityExchangeName" order="10370.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntityFileNumber" order="10390.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntityIncorporationStateCountryCode" order="10410.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntityTaxIdentificationNumber" order="10430.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntityAddressAddressLine1" order="10450.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntityAddressAddressLine2" order="10470.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntityAddressAddressLine3" order="10490.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntityAddressCityOrTown" order="10510.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntityAddressStateOrProvince" order="10530.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_EntityAddressPostalZipCode" order="10550.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_CityAreaCode" order="10570.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_LocalPhoneNumber" order="10590.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_DocumentQuarterlyReport" order="10610.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_DocumentTransitionReport" order="10630.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/StatementCondensedConsolidatedBalanceSheetsUnaudited" xlink:href="sndx-20210331.xsd#Role_StatementCondensedConsolidatedBalanceSheetsUnaudited" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/StatementCondensedConsolidatedBalanceSheetsUnaudited">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LiabilitiesAndStockholdersEquity" xlink:type="locator" xlink:label="us-gaap_LiabilitiesAndStockholdersEquity" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StockholdersEquity" xlink:type="locator" xlink:label="us-gaap_StockholdersEquity" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RetainedEarningsAccumulatedDeficit" xlink:type="locator" xlink:label="us-gaap_RetainedEarningsAccumulatedDeficit" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AccumulatedOtherComprehensiveIncomeLossAvailableForSaleSecuritiesAdjustmentNetOfTax" xlink:type="locator" xlink:label="us-gaap_AccumulatedOtherComprehensiveIncomeLossAvailableForSaleSecuritiesAdjustmentNetOfTax" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AdditionalPaidInCapitalCommonStock" xlink:type="locator" xlink:label="us-gaap_AdditionalPaidInCapitalCommonStock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CommonStockValue" xlink:type="locator" xlink:label="us-gaap_CommonStockValue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PreferredStockValue" xlink:type="locator" xlink:label="us-gaap_PreferredStockValue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StockholdersEquityAbstract" xlink:type="locator" xlink:label="us-gaap_StockholdersEquityAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CommitmentsAndContingencies" xlink:type="locator" xlink:label="us-gaap_CommitmentsAndContingencies" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_Liabilities" xlink:type="locator" xlink:label="us-gaap_Liabilities" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LiabilitiesNoncurrent" xlink:type="locator" xlink:label="us-gaap_LiabilitiesNoncurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OtherLiabilitiesNoncurrent" xlink:type="locator" xlink:label="us-gaap_OtherLiabilitiesNoncurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LongTermLoansPayable" xlink:type="locator" xlink:label="us-gaap_LongTermLoansPayable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OperatingLeaseLiabilityNoncurrent" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseLiabilityNoncurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ContractWithCustomerLiabilityNoncurrent" xlink:type="locator" xlink:label="us-gaap_ContractWithCustomerLiabilityNoncurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LiabilitiesNoncurrentAbstract" xlink:type="locator" xlink:label="us-gaap_LiabilitiesNoncurrentAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LiabilitiesCurrent" xlink:type="locator" xlink:label="us-gaap_LiabilitiesCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LoansPayableCurrent" xlink:type="locator" xlink:label="us-gaap_LoansPayableCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OperatingLeaseLiabilityCurrent" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseLiabilityCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ContractWithCustomerLiabilityCurrent" xlink:type="locator" xlink:label="us-gaap_ContractWithCustomerLiabilityCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AccruedLiabilitiesAndOtherLiabilities" xlink:type="locator" xlink:label="us-gaap_AccruedLiabilitiesAndOtherLiabilities" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AccountsPayableCurrent" xlink:type="locator" xlink:label="us-gaap_AccountsPayableCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LiabilitiesCurrentAbstract" xlink:type="locator" xlink:label="us-gaap_LiabilitiesCurrentAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:type="locator" xlink:label="us-gaap_LiabilitiesAndStockholdersEquityAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_Assets" xlink:type="locator" xlink:label="us-gaap_Assets" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OtherAssetsNoncurrent" xlink:type="locator" xlink:label="us-gaap_OtherAssetsNoncurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OperatingLeaseRightOfUseAsset" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseRightOfUseAsset" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PropertyPlantAndEquipmentNet" xlink:type="locator" xlink:label="us-gaap_PropertyPlantAndEquipmentNet" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AssetsCurrent" xlink:type="locator" xlink:label="us-gaap_AssetsCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PrepaidExpenseAndOtherAssetsCurrent" xlink:type="locator" xlink:label="us-gaap_PrepaidExpenseAndOtherAssetsCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ShortTermInvestments" xlink:type="locator" xlink:label="us-gaap_ShortTermInvestments" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RestrictedCash" xlink:type="locator" xlink:label="us-gaap_RestrictedCash" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CashAndCashEquivalentsAtCarryingValue" xlink:type="locator" xlink:label="us-gaap_CashAndCashEquivalentsAtCarryingValue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AssetsCurrentAbstract" xlink:type="locator" xlink:label="us-gaap_AssetsCurrentAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AssetsAbstract" xlink:type="locator" xlink:label="us-gaap_AssetsAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StatementOfFinancialPositionAbstract" xlink:type="locator" xlink:label="us-gaap_StatementOfFinancialPositionAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_AssetsAbstract" order="10280.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_AssetsCurrentAbstract" order="10360.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_CashAndCashEquivalentsAtCarryingValue" order="10440.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_RestrictedCash" order="10480.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_ShortTermInvestments" order="10520.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_PrepaidExpenseAndOtherAssetsCurrent" order="10560.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_AssetsCurrent" order="10600.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_PropertyPlantAndEquipmentNet" order="10640.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_OperatingLeaseRightOfUseAsset" order="10680.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_OtherAssetsNoncurrent" order="10720.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_Assets" order="10760.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_LiabilitiesAndStockholdersEquityAbstract" order="10800.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_LiabilitiesCurrentAbstract" order="10880.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_AccountsPayableCurrent" order="10960.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_AccruedLiabilitiesAndOtherLiabilities" order="11000.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_ContractWithCustomerLiabilityCurrent" order="11040.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_OperatingLeaseLiabilityCurrent" order="11080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_LoansPayableCurrent" order="11120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_LiabilitiesCurrent" order="11160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_LiabilitiesNoncurrentAbstract" order="11200.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesNoncurrentAbstract" xlink:to="us-gaap_ContractWithCustomerLiabilityNoncurrent" order="11280.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesNoncurrentAbstract" xlink:to="us-gaap_OperatingLeaseLiabilityNoncurrent" order="11320.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesNoncurrentAbstract" xlink:to="us-gaap_LongTermLoansPayable" order="11360.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesNoncurrentAbstract" xlink:to="us-gaap_OtherLiabilitiesNoncurrent" order="11400.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesNoncurrentAbstract" xlink:to="us-gaap_LiabilitiesNoncurrent" order="11440.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_Liabilities" order="11480.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_CommitmentsAndContingencies" order="11520.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_StockholdersEquityAbstract" order="11560.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StockholdersEquityAbstract" xlink:to="us-gaap_PreferredStockValue" order="11640.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StockholdersEquityAbstract" xlink:to="us-gaap_CommonStockValue" order="11680.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StockholdersEquityAbstract" xlink:to="us-gaap_AdditionalPaidInCapitalCommonStock" order="11720.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StockholdersEquityAbstract" xlink:to="us-gaap_AccumulatedOtherComprehensiveIncomeLossAvailableForSaleSecuritiesAdjustmentNetOfTax" order="11760.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StockholdersEquityAbstract" xlink:to="us-gaap_RetainedEarningsAccumulatedDeficit" order="11800.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StockholdersEquityAbstract" xlink:to="us-gaap_StockholdersEquity" order="11840.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_LiabilitiesAndStockholdersEquity" order="11880.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/StatementCondensedConsolidatedBalanceSheetsUnauditedParenthetical" xlink:href="sndx-20210331.xsd#Role_StatementCondensedConsolidatedBalanceSheetsUnauditedParenthetical" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/StatementCondensedConsolidatedBalanceSheetsUnauditedParenthetical">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CommonStockSharesOutstanding" xlink:type="locator" xlink:label="us-gaap_CommonStockSharesOutstanding" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CommonStockSharesIssued" xlink:type="locator" xlink:label="us-gaap_CommonStockSharesIssued" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CommonStockSharesAuthorized" xlink:type="locator" xlink:label="us-gaap_CommonStockSharesAuthorized" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CommonStockParOrStatedValuePerShare" xlink:type="locator" xlink:label="us-gaap_CommonStockParOrStatedValuePerShare" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PreferredStockSharesOutstanding" xlink:type="locator" xlink:label="us-gaap_PreferredStockSharesOutstanding" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PreferredStockSharesAuthorized" xlink:type="locator" xlink:label="us-gaap_PreferredStockSharesAuthorized" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PreferredStockParOrStatedValuePerShare" xlink:type="locator" xlink:label="us-gaap_PreferredStockParOrStatedValuePerShare" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StatementOfFinancialPositionAbstract" xlink:type="locator" xlink:label="us-gaap_StatementOfFinancialPositionAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_PreferredStockParOrStatedValuePerShare" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_PreferredStockSharesAuthorized" order="10050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_PreferredStockSharesOutstanding" order="10090.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_CommonStockParOrStatedValuePerShare" order="10130.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_CommonStockSharesAuthorized" order="10170.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_CommonStockSharesIssued" order="10210.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_CommonStockSharesOutstanding" order="10250.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/StatementCondensedConsolidatedStatementsOfComprehensiveLossUnaudited" xlink:href="sndx-20210331.xsd#Role_StatementCondensedConsolidatedStatementsOfComprehensiveLossUnaudited" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/StatementCondensedConsolidatedStatementsOfComprehensiveLossUnaudited">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_WeightedAverageNumberOfShareOutstandingBasicAndDiluted" xlink:type="locator" xlink:label="us-gaap_WeightedAverageNumberOfShareOutstandingBasicAndDiluted" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EarningsPerShareBasicAndDiluted" xlink:type="locator" xlink:label="us-gaap_EarningsPerShareBasicAndDiluted" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NetIncomeLossAvailableToCommonStockholdersBasic" xlink:type="locator" xlink:label="us-gaap_NetIncomeLossAvailableToCommonStockholdersBasic" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ComprehensiveIncomeNetOfTax" xlink:type="locator" xlink:label="us-gaap_ComprehensiveIncomeNetOfTax" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" xlink:type="locator" xlink:label="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OtherComprehensiveIncomeLossNetOfTaxPeriodIncreaseDecreaseAbstract" xlink:type="locator" xlink:label="us-gaap_OtherComprehensiveIncomeLossNetOfTaxPeriodIncreaseDecreaseAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NetIncomeLoss" xlink:type="locator" xlink:label="us-gaap_NetIncomeLoss" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NonoperatingIncomeExpense" xlink:type="locator" xlink:label="us-gaap_NonoperatingIncomeExpense" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OtherNonoperatingIncomeExpense" xlink:type="locator" xlink:label="us-gaap_OtherNonoperatingIncomeExpense" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_InvestmentIncomeInterest" xlink:type="locator" xlink:label="us-gaap_InvestmentIncomeInterest" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_InterestExpense" xlink:type="locator" xlink:label="us-gaap_InterestExpense" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NonoperatingIncomeExpenseAbstract" xlink:type="locator" xlink:label="us-gaap_NonoperatingIncomeExpenseAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OperatingIncomeLoss" xlink:type="locator" xlink:label="us-gaap_OperatingIncomeLoss" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OperatingExpenses" xlink:type="locator" xlink:label="us-gaap_OperatingExpenses" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_GeneralAndAdministrativeExpense" xlink:type="locator" xlink:label="us-gaap_GeneralAndAdministrativeExpense" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ResearchAndDevelopmentExpense" xlink:type="locator" xlink:label="us-gaap_ResearchAndDevelopmentExpense" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OperatingExpensesAbstract" xlink:type="locator" xlink:label="us-gaap_OperatingExpensesAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_TypeOfRevenueExtensibleList" xlink:type="locator" xlink:label="us-gaap_TypeOfRevenueExtensibleList" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RevenuesAbstract" xlink:type="locator" xlink:label="us-gaap_RevenuesAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StatementOfIncomeAndComprehensiveIncomeAbstract" xlink:type="locator" xlink:label="us-gaap_StatementOfIncomeAndComprehensiveIncomeAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfIncomeAndComprehensiveIncomeAbstract" xlink:to="us-gaap_RevenuesAbstract" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RevenuesAbstract" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" order="10200.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RevenuesAbstract" xlink:to="us-gaap_TypeOfRevenueExtensibleList" order="10240.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfIncomeAndComprehensiveIncomeAbstract" xlink:to="us-gaap_OperatingExpensesAbstract" order="10320.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingExpensesAbstract" xlink:to="us-gaap_ResearchAndDevelopmentExpense" order="10400.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingExpensesAbstract" xlink:to="us-gaap_GeneralAndAdministrativeExpense" order="10440.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingExpensesAbstract" xlink:to="us-gaap_OperatingExpenses" order="10480.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfIncomeAndComprehensiveIncomeAbstract" xlink:to="us-gaap_OperatingIncomeLoss" order="10520.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfIncomeAndComprehensiveIncomeAbstract" xlink:to="us-gaap_NonoperatingIncomeExpenseAbstract" order="10560.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NonoperatingIncomeExpenseAbstract" xlink:to="us-gaap_InterestExpense" order="10640.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NonoperatingIncomeExpenseAbstract" xlink:to="us-gaap_InvestmentIncomeInterest" order="10680.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NonoperatingIncomeExpenseAbstract" xlink:to="us-gaap_OtherNonoperatingIncomeExpense" order="10720.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NonoperatingIncomeExpenseAbstract" xlink:to="us-gaap_NonoperatingIncomeExpense" order="10760.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfIncomeAndComprehensiveIncomeAbstract" xlink:to="us-gaap_NetIncomeLoss" order="10800.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfIncomeAndComprehensiveIncomeAbstract" xlink:to="us-gaap_OtherComprehensiveIncomeLossNetOfTaxPeriodIncreaseDecreaseAbstract" order="10840.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OtherComprehensiveIncomeLossNetOfTaxPeriodIncreaseDecreaseAbstract" xlink:to="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" order="10920.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OtherComprehensiveIncomeLossNetOfTaxPeriodIncreaseDecreaseAbstract" xlink:to="us-gaap_ComprehensiveIncomeNetOfTax" order="10960.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfIncomeAndComprehensiveIncomeAbstract" xlink:to="us-gaap_NetIncomeLossAvailableToCommonStockholdersBasic" order="11000.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfIncomeAndComprehensiveIncomeAbstract" xlink:to="us-gaap_EarningsPerShareBasicAndDiluted" order="11040.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfIncomeAndComprehensiveIncomeAbstract" xlink:to="us-gaap_WeightedAverageNumberOfShareOutstandingBasicAndDiluted" order="11080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/StatementCondensedConsolidatedStatementsOfCashFlowsUnaudited" xlink:href="sndx-20210331.xsd#Role_StatementCondensedConsolidatedStatementsOfCashFlowsUnaudited" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/StatementCondensedConsolidatedStatementsOfCashFlowsUnaudited">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DebtIssuanceCostsIncurredDuringNoncashOrPartialNoncashTransaction" xlink:type="locator" xlink:label="us-gaap_DebtIssuanceCostsIncurredDuringNoncashOrPartialNoncashTransaction" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NoncashInvestingAndFinancingItemsAbstract" xlink:type="locator" xlink:label="us-gaap_NoncashInvestingAndFinancingItemsAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_InterestPaidNet" xlink:type="locator" xlink:label="us-gaap_InterestPaidNet" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_SupplementalCashFlowInformationAbstract" xlink:type="locator" xlink:label="us-gaap_SupplementalCashFlowInformationAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations" xlink:type="locator" xlink:label="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations_li0l2" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations" xlink:type="locator" xlink:label="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:type="locator" xlink:label="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInFinancingActivities" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ProceedsFromStockOptionsExercised" xlink:type="locator" xlink:label="us-gaap_ProceedsFromStockOptionsExercised" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ProceedsFromStockPlans" xlink:type="locator" xlink:label="us-gaap_ProceedsFromStockPlans" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ProceedsFromDebtNetOfIssuanceCosts" xlink:type="locator" xlink:label="us-gaap_ProceedsFromDebtNetOfIssuanceCosts" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ProceedsFromIssuanceOfCommonStock" xlink:type="locator" xlink:label="us-gaap_ProceedsFromIssuanceOfCommonStock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInInvestingActivities" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ProceedsFromSaleAndMaturityOfAvailableForSaleSecurities" xlink:type="locator" xlink:label="us-gaap_ProceedsFromSaleAndMaturityOfAvailableForSaleSecurities" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PaymentsToAcquireShortTermInvestments" xlink:type="locator" xlink:label="us-gaap_PaymentsToAcquireShortTermInvestments" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInOperatingActivities" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_IncreaseDecreaseInAccruedLiabilitiesAndOtherOperatingLiabilities" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInAccruedLiabilitiesAndOtherOperatingLiabilities" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_IncreaseDecreaseInContractWithCustomerLiability" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInContractWithCustomerLiability" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_IncreaseDecreaseInAccountsPayable" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInAccountsPayable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ShareBasedCompensation" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensation" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PaidInKindInterest" xlink:type="locator" xlink:label="us-gaap_PaidInKindInterest" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_NoncashOperatingLeaseExpense" xlink:type="locator" xlink:label="sndx_NoncashOperatingLeaseExpense" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments" xlink:type="locator" xlink:label="us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_DepreciationAndRelatedAdjustment" xlink:type="locator" xlink:label="sndx_DepreciationAndRelatedAdjustment" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:type="locator" xlink:label="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ProfitLoss" xlink:type="locator" xlink:label="us-gaap_ProfitLoss" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NetCashProvidedByUsedInOperatingActivitiesAbstract" xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInOperatingActivitiesAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StatementLineItems" xlink:type="locator" xlink:label="us-gaap_StatementLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PrivatePlacementMember" xlink:type="locator" xlink:label="us-gaap_PrivatePlacementMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_SaleOfStockNameOfTransactionDomain" xlink:type="locator" xlink:label="us-gaap_SaleOfStockNameOfTransactionDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_SubsidiarySaleOfStockAxis" xlink:type="locator" xlink:label="us-gaap_SubsidiarySaleOfStockAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StatementTable" xlink:type="locator" xlink:label="us-gaap_StatementTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StatementOfCashFlowsAbstract" xlink:type="locator" xlink:label="us-gaap_StatementOfCashFlowsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="us-gaap_StatementTable" order="10210.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_SubsidiarySaleOfStockAxis" order="10220.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SubsidiarySaleOfStockAxis" xlink:to="us-gaap_SaleOfStockNameOfTransactionDomain" order="10250.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SaleOfStockNameOfTransactionDomain" xlink:to="us-gaap_PrivatePlacementMember" order="10270.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementLineItems" order="10290.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_NetCashProvidedByUsedInOperatingActivitiesAbstract" order="10300.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_ProfitLoss" order="10380.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" order="10420.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="sndx_DepreciationAndRelatedAdjustment" order="10500.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments" order="10540.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="sndx_NoncashOperatingLeaseExpense" order="10580.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_PaidInKindInterest" order="10620.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_ShareBasedCompensation" order="10660.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" order="10700.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" order="10780.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInAccountsPayable" order="10820.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInContractWithCustomerLiability" order="10860.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInAccruedLiabilitiesAndOtherOperatingLiabilities" order="10900.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_NetCashProvidedByUsedInOperatingActivities" order="10940.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" order="10980.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" xlink:to="us-gaap_PaymentsToAcquireShortTermInvestments" order="11060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" xlink:to="us-gaap_ProceedsFromSaleAndMaturityOfAvailableForSaleSecurities" order="11100.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" xlink:to="us-gaap_NetCashProvidedByUsedInInvestingActivities" order="11140.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" order="11180.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" xlink:to="us-gaap_ProceedsFromIssuanceOfCommonStock" order="11260.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" xlink:to="us-gaap_ProceedsFromDebtNetOfIssuanceCosts" order="11300.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" xlink:to="us-gaap_ProceedsFromStockPlans" order="11340.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" xlink:to="us-gaap_ProceedsFromStockOptionsExercised" order="11380.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" xlink:to="us-gaap_NetCashProvidedByUsedInFinancingActivities" order="11420.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" order="11460.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations" order="11500.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations_li0l2" order="11540.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_SupplementalCashFlowInformationAbstract" order="11580.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SupplementalCashFlowInformationAbstract" xlink:to="us-gaap_InterestPaidNet" order="11660.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_NoncashInvestingAndFinancingItemsAbstract" order="11700.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NoncashInvestingAndFinancingItemsAbstract" xlink:to="us-gaap_DebtIssuanceCostsIncurredDuringNoncashOrPartialNoncashTransaction" order="11780.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureNatureOfBusiness" xlink:href="sndx-20210331.xsd#Role_DisclosureNatureOfBusiness" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureNatureOfBusiness">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NatureOfOperations" xlink:type="locator" xlink:label="us-gaap_NatureOfOperations" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:type="locator" xlink:label="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:to="us-gaap_NatureOfOperations" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureBasisOfPresentation" xlink:href="sndx-20210331.xsd#Role_DisclosureBasisOfPresentation" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureBasisOfPresentation">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_BusinessDescriptionAndBasisOfPresentationTextBlock" xlink:type="locator" xlink:label="us-gaap_BusinessDescriptionAndBasisOfPresentationTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AccountingPoliciesAbstract" xlink:type="locator" xlink:label="us-gaap_AccountingPoliciesAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_BusinessDescriptionAndBasisOfPresentationTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureSummaryOfSignificantAccountingPolicies" xlink:href="sndx-20210331.xsd#Role_DisclosureSummaryOfSignificantAccountingPolicies" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureSummaryOfSignificantAccountingPolicies">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_SignificantAccountingPoliciesTextBlock" xlink:type="locator" xlink:label="us-gaap_SignificantAccountingPoliciesTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AccountingPoliciesAbstract" xlink:type="locator" xlink:label="us-gaap_AccountingPoliciesAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_SignificantAccountingPoliciesTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureRevenueFromContractsWithCustomers" xlink:href="sndx-20210331.xsd#Role_DisclosureRevenueFromContractsWithCustomers" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureRevenueFromContractsWithCustomers">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RevenueFromContractWithCustomerTextBlock" xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RevenueFromContractWithCustomerAbstract" xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RevenueFromContractWithCustomerAbstract" xlink:to="us-gaap_RevenueFromContractWithCustomerTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureNetLossPerShareAttributableToCommonStockholders" xlink:href="sndx-20210331.xsd#Role_DisclosureNetLossPerShareAttributableToCommonStockholders" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureNetLossPerShareAttributableToCommonStockholders">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EarningsPerShareTextBlock" xlink:type="locator" xlink:label="us-gaap_EarningsPerShareTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EarningsPerShareAbstract" xlink:type="locator" xlink:label="us-gaap_EarningsPerShareAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareAbstract" xlink:to="us-gaap_EarningsPerShareTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureSignificantAgreements" xlink:href="sndx-20210331.xsd#Role_DisclosureSignificantAgreements" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureSignificantAgreements">
    <link:loc xlink:href="sndx-20210331.xsd#sndx_SignificantAgreementsDisclosureTextBlock" xlink:type="locator" xlink:label="sndx_SignificantAgreementsDisclosureTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EquityAbstract" xlink:type="locator" xlink:label="us-gaap_EquityAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityAbstract" xlink:to="sndx_SignificantAgreementsDisclosureTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureFairValueMeasurements" xlink:href="sndx-20210331.xsd#Role_DisclosureFairValueMeasurements" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureFairValueMeasurements">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueMeasurementInputsDisclosureTextBlock" xlink:type="locator" xlink:label="us-gaap_FairValueMeasurementInputsDisclosureTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueDisclosuresAbstract" xlink:type="locator" xlink:label="us-gaap_FairValueDisclosuresAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueDisclosuresAbstract" xlink:to="us-gaap_FairValueMeasurementInputsDisclosureTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosurePrepaidExpensesAndOtherCurrentAssets" xlink:href="sndx-20210331.xsd#Role_DisclosurePrepaidExpensesAndOtherCurrentAssets" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosurePrepaidExpensesAndOtherCurrentAssets">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OtherCurrentAssetsTextBlock" xlink:type="locator" xlink:label="us-gaap_OtherCurrentAssetsTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureAbstract" xlink:type="locator" xlink:label="us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureAbstract" xlink:to="us-gaap_OtherCurrentAssetsTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureAccruedExpensesAndOtherCurrentLiabilities" xlink:href="sndx-20210331.xsd#Role_DisclosureAccruedExpensesAndOtherCurrentLiabilities" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureAccruedExpensesAndOtherCurrentLiabilities">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AccountsPayableAccruedLiabilitiesAndOtherLiabilitiesDisclosureCurrentTextBlock" xlink:type="locator" xlink:label="us-gaap_AccountsPayableAccruedLiabilitiesAndOtherLiabilitiesDisclosureCurrentTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PayablesAndAccrualsAbstract" xlink:type="locator" xlink:label="us-gaap_PayablesAndAccrualsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PayablesAndAccrualsAbstract" xlink:to="us-gaap_AccountsPayableAccruedLiabilitiesAndOtherLiabilitiesDisclosureCurrentTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockBasedCompensation" xlink:href="sndx-20210331.xsd#Role_DisclosureStockBasedCompensation" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockBasedCompensation">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock" xlink:type="locator" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:type="locator" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:to="us-gaap_DisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureLoanPayable" xlink:href="sndx-20210331.xsd#Role_DisclosureLoanPayable" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureLoanPayable">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DebtDisclosureTextBlock" xlink:type="locator" xlink:label="us-gaap_DebtDisclosureTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DebtDisclosureAbstract" xlink:type="locator" xlink:label="us-gaap_DebtDisclosureAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtDisclosureAbstract" xlink:to="us-gaap_DebtDisclosureTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockholdersEquity" xlink:href="sndx-20210331.xsd#Role_DisclosureStockholdersEquity" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockholdersEquity">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StockholdersEquityNoteDisclosureTextBlock" xlink:type="locator" xlink:label="us-gaap_StockholdersEquityNoteDisclosureTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EquityAbstract" xlink:type="locator" xlink:label="us-gaap_EquityAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityAbstract" xlink:to="us-gaap_StockholdersEquityNoteDisclosureTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureBasisOfPresentationPolicies" xlink:href="sndx-20210331.xsd#Role_DisclosureBasisOfPresentationPolicies" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureBasisOfPresentationPolicies">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_UseOfEstimates" xlink:type="locator" xlink:label="us-gaap_UseOfEstimates" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_SignificantRisksAndUncertaintiesPolicyTextBlock" xlink:type="locator" xlink:label="sndx_SignificantRisksAndUncertaintiesPolicyTextBlock" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_SignificantAccountingPoliciesPolicyTextBlock" xlink:type="locator" xlink:label="sndx_SignificantAccountingPoliciesPolicyTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ConsolidationPolicyTextBlock" xlink:type="locator" xlink:label="us-gaap_ConsolidationPolicyTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AccountingPoliciesAbstract" xlink:type="locator" xlink:label="us-gaap_AccountingPoliciesAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_ConsolidationPolicyTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="sndx_SignificantAccountingPoliciesPolicyTextBlock" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="sndx_SignificantRisksAndUncertaintiesPolicyTextBlock" order="10050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_UseOfEstimates" order="10070.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureNetLossPerShareAttributableToCommonStockholdersTables" xlink:href="sndx-20210331.xsd#Role_DisclosureNetLossPerShareAttributableToCommonStockholdersTables" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureNetLossPerShareAttributableToCommonStockholdersTables">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTextBlock" xlink:type="locator" xlink:label="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfEarningsPerShareBasicAndDilutedTableTextBlock" xlink:type="locator" xlink:label="us-gaap_ScheduleOfEarningsPerShareBasicAndDilutedTableTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EarningsPerShareAbstract" xlink:type="locator" xlink:label="us-gaap_EarningsPerShareAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareAbstract" xlink:to="us-gaap_ScheduleOfEarningsPerShareBasicAndDilutedTableTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareAbstract" xlink:to="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTextBlock" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureFairValueMeasurementsTables" xlink:href="sndx-20210331.xsd#Role_DisclosureFairValueMeasurementsTables" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureFairValueMeasurementsTables">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DebtSecuritiesAvailableForSaleTableTextBlock" xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleTableTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfFairValueAssetsAndLiabilitiesMeasuredOnRecurringBasisTableTextBlock" xlink:type="locator" xlink:label="us-gaap_ScheduleOfFairValueAssetsAndLiabilitiesMeasuredOnRecurringBasisTableTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueDisclosuresAbstract" xlink:type="locator" xlink:label="us-gaap_FairValueDisclosuresAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueDisclosuresAbstract" xlink:to="us-gaap_ScheduleOfFairValueAssetsAndLiabilitiesMeasuredOnRecurringBasisTableTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueDisclosuresAbstract" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleTableTextBlock" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosurePrepaidExpensesAndOtherCurrentAssetsTables" xlink:href="sndx-20210331.xsd#Role_DisclosurePrepaidExpensesAndOtherCurrentAssetsTables" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosurePrepaidExpensesAndOtherCurrentAssetsTables">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureTextBlock" xlink:type="locator" xlink:label="us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureAbstract" xlink:type="locator" xlink:label="us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureAbstract" xlink:to="us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureAccruedExpensesAndOtherCurrentLiabilitiesTables" xlink:href="sndx-20210331.xsd#Role_DisclosureAccruedExpensesAndOtherCurrentLiabilitiesTables" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureAccruedExpensesAndOtherCurrentLiabilitiesTables">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfAccountsPayableAndAccruedLiabilitiesTableTextBlock" xlink:type="locator" xlink:label="us-gaap_ScheduleOfAccountsPayableAndAccruedLiabilitiesTableTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PayablesAndAccrualsAbstract" xlink:type="locator" xlink:label="us-gaap_PayablesAndAccrualsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PayablesAndAccrualsAbstract" xlink:to="us-gaap_ScheduleOfAccountsPayableAndAccruedLiabilitiesTableTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockBasedCompensationTables" xlink:href="sndx-20210331.xsd#Role_DisclosureStockBasedCompensationTables" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockBasedCompensationTables">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DisclosureOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTextBlock" xlink:type="locator" xlink:label="us-gaap_DisclosureOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTextBlock" xlink:type="locator" xlink:label="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:type="locator" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:to="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:to="us-gaap_DisclosureOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTextBlock" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureLoanPayableTables" xlink:href="sndx-20210331.xsd#Role_DisclosureLoanPayableTables" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureLoanPayableTables">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfMaturitiesOfLongTermDebtTableTextBlock" xlink:type="locator" xlink:label="us-gaap_ScheduleOfMaturitiesOfLongTermDebtTableTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DebtDisclosureAbstract" xlink:type="locator" xlink:label="us-gaap_DebtDisclosureAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtDisclosureAbstract" xlink:to="us-gaap_ScheduleOfMaturitiesOfLongTermDebtTableTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockholdersEquityTables" xlink:href="sndx-20210331.xsd#Role_DisclosureStockholdersEquityTables" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockholdersEquityTables">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfStockholdersEquityNoteWarrantsOrRightsTextBlock" xlink:type="locator" xlink:label="us-gaap_ScheduleOfStockholdersEquityNoteWarrantsOrRightsTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfStockholdersEquityTableTextBlock" xlink:type="locator" xlink:label="us-gaap_ScheduleOfStockholdersEquityTableTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EquityAbstract" xlink:type="locator" xlink:label="us-gaap_EquityAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityAbstract" xlink:to="us-gaap_ScheduleOfStockholdersEquityTableTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityAbstract" xlink:to="us-gaap_ScheduleOfStockholdersEquityNoteWarrantsOrRightsTextBlock" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureNatureOfBusinessAdditionalInformationDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureNatureOfBusinessAdditionalInformationDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureNatureOfBusinessAdditionalInformationDetail">
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityIncorporationStateCountryCode" xlink:type="locator" xlink:label="dei_EntityIncorporationStateCountryCode" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityIncorporationDateOfIncorporation" xlink:type="locator" xlink:label="dei_EntityIncorporationDateOfIncorporation" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NumberOfOperatingSegments" xlink:type="locator" xlink:label="us-gaap_NumberOfOperatingSegments" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:type="locator" xlink:label="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:to="us-gaap_NumberOfOperatingSegments" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:to="dei_EntityIncorporationDateOfIncorporation" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:to="dei_EntityIncorporationStateCountryCode" order="10050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureRevenueFromContractWithCustomersAdditionalInformationDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureRevenueFromContractWithCustomersAdditionalInformationDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureRevenueFromContractWithCustomersAdditionalInformationDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ContractWithCustomerLiability" xlink:type="locator" xlink:label="us-gaap_ContractWithCustomerLiability" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RevenueRemainingPerformanceObligationExpectedTimingOfSatisfactionYear1" xlink:type="locator" xlink:label="us-gaap_RevenueRemainingPerformanceObligationExpectedTimingOfSatisfactionYear1" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RevenueRemainingPerformanceObligation" xlink:type="locator" xlink:label="us-gaap_RevenueRemainingPerformanceObligation" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ContractWithCustomerLiabilityRevenueRecognized" xlink:type="locator" xlink:label="us-gaap_ContractWithCustomerLiabilityRevenueRecognized" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_RevenueFromContractWithCustomerMilestoneMethodFactors" xlink:type="locator" xlink:label="sndx_RevenueFromContractWithCustomerMilestoneMethodFactors" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_UpfrontPaymentAllocatedToLicenseFee" xlink:type="locator" xlink:label="sndx_UpfrontPaymentAllocatedToLicenseFee" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_UpfrontPaymentAllocatedToEquityPurchaseFairValue" xlink:type="locator" xlink:label="sndx_UpfrontPaymentAllocatedToEquityPurchaseFairValue" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_PeriodOfTerminationAfterFirstCommercialSaleOfFirstLicensedProduct" xlink:type="locator" xlink:label="sndx_PeriodOfTerminationAfterFirstCommercialSaleOfFirstLicensedProduct" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_PotentialMilestonePaymentsReceivable" xlink:type="locator" xlink:label="sndx_PotentialMilestonePaymentsReceivable" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_NonRefundableUpFrontPaymentReceived" xlink:type="locator" xlink:label="sndx_NonRefundableUpFrontPaymentReceived" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_UpfrontPaymentAllocatedToEquityPurchase" xlink:type="locator" xlink:label="sndx_UpfrontPaymentAllocatedToEquityPurchase" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_UpfrontPaymentsReceived" xlink:type="locator" xlink:label="sndx_UpfrontPaymentsReceived" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleLineItems" xlink:type="locator" xlink:label="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_MinimumMember" xlink:type="locator" xlink:label="srt_MinimumMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_MaximumMember" xlink:type="locator" xlink:label="srt_MaximumMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_RangeMember" xlink:type="locator" xlink:label="srt_RangeMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_RangeAxis" xlink:type="locator" xlink:label="srt_RangeAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_KyowaKirinCoLtdMember" xlink:type="locator" xlink:label="sndx_KyowaKirinCoLtdMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_RepurchaseAgreementCounterpartyNameDomain" xlink:type="locator" xlink:label="srt_RepurchaseAgreementCounterpartyNameDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_CounterpartyNameAxis" xlink:type="locator" xlink:label="srt_CounterpartyNameAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_LicenseAgreementMember" xlink:type="locator" xlink:label="sndx_LicenseAgreementMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:type="locator" xlink:label="us-gaap_ArrangementsAndNonarrangementTransactionsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_TypeOfArrangementAxis" xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleTable" xlink:type="locator" xlink:label="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AccountingChangesAndErrorCorrectionsAbstract" xlink:type="locator" xlink:label="us-gaap_AccountingChangesAndErrorCorrectionsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingChangesAndErrorCorrectionsAbstract" xlink:to="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="us-gaap_ArrangementsAndNonarrangementTransactionsMember" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:to="sndx_LicenseAgreementMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleTable" xlink:to="srt_CounterpartyNameAxis" order="10030.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_CounterpartyNameAxis" xlink:to="srt_RepurchaseAgreementCounterpartyNameDomain" order="10200.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RepurchaseAgreementCounterpartyNameDomain" xlink:to="sndx_KyowaKirinCoLtdMember" order="10220.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleTable" xlink:to="srt_RangeAxis" order="10030.04" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" order="10340.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" order="10360.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeMember" xlink:to="srt_MinimumMember" order="10380.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleTable" xlink:to="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleLineItems" order="10920.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleLineItems" xlink:to="sndx_UpfrontPaymentsReceived" order="10930.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleLineItems" xlink:to="sndx_UpfrontPaymentAllocatedToEquityPurchase" order="10950.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleLineItems" xlink:to="sndx_NonRefundableUpFrontPaymentReceived" order="10970.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleLineItems" xlink:to="sndx_PotentialMilestonePaymentsReceivable" order="10990.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleLineItems" xlink:to="sndx_PeriodOfTerminationAfterFirstCommercialSaleOfFirstLicensedProduct" order="11010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleLineItems" xlink:to="sndx_UpfrontPaymentAllocatedToEquityPurchaseFairValue" order="11060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleLineItems" xlink:to="sndx_UpfrontPaymentAllocatedToLicenseFee" order="11100.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleLineItems" xlink:to="sndx_RevenueFromContractWithCustomerMilestoneMethodFactors" order="11170.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleLineItems" xlink:to="us-gaap_ContractWithCustomerLiabilityRevenueRecognized" order="11210.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleLineItems" xlink:to="us-gaap_RevenueRemainingPerformanceObligation" order="11280.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleLineItems" xlink:to="us-gaap_RevenueRemainingPerformanceObligationExpectedTimingOfSatisfactionYear1" order="11300.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NewAccountingPronouncementsOrChangeInAccountingPrincipleLineItems" xlink:to="us-gaap_ContractWithCustomerLiability" order="11370.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureNetLossPerShareAttributableToCommonStockholdersComputationOfBasicAndDilutedNetLossPerShareAttributableToCommonStockholdersDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureNetLossPerShareAttributableToCommonStockholdersComputationOfBasicAndDilutedNetLossPerShareAttributableToCommonStockholdersDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureNetLossPerShareAttributableToCommonStockholdersComputationOfBasicAndDilutedNetLossPerShareAttributableToCommonStockholdersDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_WeightedAverageNumberOfShareOutstandingBasicAndDiluted" xlink:type="locator" xlink:label="us-gaap_WeightedAverageNumberOfShareOutstandingBasicAndDiluted" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_WeightedAverageNumberOfSharesOutstandingAbstract" xlink:type="locator" xlink:label="us-gaap_WeightedAverageNumberOfSharesOutstandingAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EarningsPerShareBasicAndDiluted" xlink:type="locator" xlink:label="us-gaap_EarningsPerShareBasicAndDiluted" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NetIncomeLossAvailableToCommonStockholdersBasic" xlink:type="locator" xlink:label="us-gaap_NetIncomeLossAvailableToCommonStockholdersBasic" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_Dividends" xlink:type="locator" xlink:label="us-gaap_Dividends" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NetIncomeLoss" xlink:type="locator" xlink:label="us-gaap_NetIncomeLoss" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NetIncomeLossAbstract" xlink:type="locator" xlink:label="us-gaap_NetIncomeLossAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EarningsPerShareBasicLineItems" xlink:type="locator" xlink:label="us-gaap_EarningsPerShareBasicLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_WarrantMember" xlink:type="locator" xlink:label="us-gaap_WarrantMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AntidilutiveSecuritiesNameDomain" xlink:type="locator" xlink:label="us-gaap_AntidilutiveSecuritiesNameDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:type="locator" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EarningsPerShareAbstract" xlink:type="locator" xlink:label="us-gaap_EarningsPerShareAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareAbstract" xlink:to="us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" order="10040.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" xlink:to="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" order="10050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:to="us-gaap_AntidilutiveSecuritiesNameDomain" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="us-gaap_WarrantMember" order="10100.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" xlink:to="us-gaap_EarningsPerShareBasicLineItems" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareBasicLineItems" xlink:to="us-gaap_NetIncomeLossAbstract" order="10130.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetIncomeLossAbstract" xlink:to="us-gaap_NetIncomeLoss" order="10210.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetIncomeLossAbstract" xlink:to="us-gaap_Dividends" order="10250.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetIncomeLossAbstract" xlink:to="us-gaap_NetIncomeLossAvailableToCommonStockholdersBasic" order="10290.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetIncomeLossAbstract" xlink:to="us-gaap_EarningsPerShareBasicAndDiluted" order="10330.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareBasicLineItems" xlink:to="us-gaap_WeightedAverageNumberOfSharesOutstandingAbstract" order="10370.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_WeightedAverageNumberOfSharesOutstandingAbstract" xlink:to="us-gaap_WeightedAverageNumberOfShareOutstandingBasicAndDiluted" order="10450.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureNetLossPerShareAttributableToCommonStockholdersPotentialDilutiveSecuritiesExcludedFromComputationOfDilutedNetLossPerCommonShareDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureNetLossPerShareAttributableToCommonStockholdersPotentialDilutiveSecuritiesExcludedFromComputationOfDilutedNetLossPerCommonShareDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureNetLossPerShareAttributableToCommonStockholdersPotentialDilutiveSecuritiesExcludedFromComputationOfDilutedNetLossPerCommonShareDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount" xlink:type="locator" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" xlink:type="locator" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RestrictedStockUnitsRSUMember" xlink:type="locator" xlink:label="us-gaap_RestrictedStockUnitsRSUMember" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_EmployeeStockPurchasePlanMember" xlink:type="locator" xlink:label="sndx_EmployeeStockPurchasePlanMember" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_WarrantsToPurchaseCommonStockMember" xlink:type="locator" xlink:label="sndx_WarrantsToPurchaseCommonStockMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EmployeeStockOptionMember" xlink:type="locator" xlink:label="us-gaap_EmployeeStockOptionMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AntidilutiveSecuritiesNameDomain" xlink:type="locator" xlink:label="us-gaap_AntidilutiveSecuritiesNameDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:type="locator" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EarningsPerShareAbstract" xlink:type="locator" xlink:label="us-gaap_EarningsPerShareAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareAbstract" xlink:to="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" xlink:to="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:to="us-gaap_AntidilutiveSecuritiesNameDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="us-gaap_EmployeeStockOptionMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="sndx_WarrantsToPurchaseCommonStockMember" order="10100.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="sndx_EmployeeStockPurchasePlanMember" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="us-gaap_RestrictedStockUnitsRSUMember" order="10140.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" xlink:to="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" order="10160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" xlink:to="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount" order="10170.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureNetLossPerShareAttributableToCommonStockholdersAdditionalInformationDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureNetLossPerShareAttributableToCommonStockholdersAdditionalInformationDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureNetLossPerShareAttributableToCommonStockholdersAdditionalInformationDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ClassOfWarrantOrRightOutstanding" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightOutstanding" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_NumberOfPreFundedWarrantsExchangedForCommonStock" xlink:type="locator" xlink:label="sndx_NumberOfPreFundedWarrantsExchangedForCommonStock" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_ClassOfWarrantOrRightIssued" xlink:type="locator" xlink:label="sndx_ClassOfWarrantOrRightIssued" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues" xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodSharesNewIssues" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_NumberOfCommonStockWarrantsIssued" xlink:type="locator" xlink:label="sndx_NumberOfCommonStockWarrantsIssued" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_NumberOfCommonStockConvertedToWarrants" xlink:type="locator" xlink:label="sndx_NumberOfCommonStockConvertedToWarrants" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EarningsPerShareBasicLineItems" xlink:type="locator" xlink:label="us-gaap_EarningsPerShareBasicLineItems" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_BiotechnologyValueFundLPMember" xlink:type="locator" xlink:label="sndx_BiotechnologyValueFundLPMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_RepurchaseAgreementCounterpartyNameDomain" xlink:type="locator" xlink:label="srt_RepurchaseAgreementCounterpartyNameDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_CounterpartyNameAxis" xlink:type="locator" xlink:label="srt_CounterpartyNameAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_SeriesOneAndSeriesTwoWarrantsMember" xlink:type="locator" xlink:label="sndx_SeriesOneAndSeriesTwoWarrantsMember" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_PreFundedWarrantsMember" xlink:type="locator" xlink:label="sndx_PreFundedWarrantsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EquityComponentDomain" xlink:type="locator" xlink:label="us-gaap_EquityComponentDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StatementEquityComponentsAxis" xlink:type="locator" xlink:label="us-gaap_StatementEquityComponentsAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EarningsPerShareAbstract" xlink:type="locator" xlink:label="us-gaap_EarningsPerShareAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareAbstract" xlink:to="us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" xlink:to="us-gaap_StatementEquityComponentsAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="sndx_PreFundedWarrantsMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="sndx_SeriesOneAndSeriesTwoWarrantsMember" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" xlink:to="srt_CounterpartyNameAxis" order="10030.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_CounterpartyNameAxis" xlink:to="srt_RepurchaseAgreementCounterpartyNameDomain" order="10160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RepurchaseAgreementCounterpartyNameDomain" xlink:to="sndx_BiotechnologyValueFundLPMember" order="10180.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfEarningsPerShareBasicByCommonClassTable" xlink:to="us-gaap_EarningsPerShareBasicLineItems" order="10280.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareBasicLineItems" xlink:to="sndx_NumberOfCommonStockConvertedToWarrants" order="10290.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareBasicLineItems" xlink:to="sndx_NumberOfCommonStockWarrantsIssued" order="10350.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareBasicLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesNewIssues" order="10410.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareBasicLineItems" xlink:to="us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" order="10470.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareBasicLineItems" xlink:to="sndx_ClassOfWarrantOrRightIssued" order="10530.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareBasicLineItems" xlink:to="sndx_NumberOfPreFundedWarrantsExchangedForCommonStock" order="10680.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareBasicLineItems" xlink:to="us-gaap_ClassOfWarrantOrRightOutstanding" order="10700.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureSignificantAgreementsAdditionalInformationDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureSignificantAgreementsAdditionalInformationDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureSignificantAgreementsAdditionalInformationDetail">
    <link:loc xlink:href="sndx-20210331.xsd#sndx_UpfrontLicenseFeesPaid" xlink:type="locator" xlink:label="sndx_UpfrontLicenseFeesPaid" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_AccruedContractualObligation" xlink:type="locator" xlink:label="sndx_AccruedContractualObligation" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_ContractualObligationsTerm" xlink:type="locator" xlink:label="sndx_ContractualObligationsTerm" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_RemainingContractualObligation" xlink:type="locator" xlink:label="sndx_RemainingContractualObligation" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ContractualObligation" xlink:type="locator" xlink:label="us-gaap_ContractualObligation" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_IncreaseDecreaseInContractualObligation" xlink:type="locator" xlink:label="sndx_IncreaseDecreaseInContractualObligation" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_MilestonePaymentDue" xlink:type="locator" xlink:label="sndx_MilestonePaymentDue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ResearchAndDevelopmentExpense" xlink:type="locator" xlink:label="us-gaap_ResearchAndDevelopmentExpense" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_LicenseAgreementsExpirationPeriod" xlink:type="locator" xlink:label="sndx_LicenseAgreementsExpirationPeriod" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_AggregatePotentialMilestonePayable" xlink:type="locator" xlink:label="sndx_AggregatePotentialMilestonePayable" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_PotentialMilestonePaymentsUponAchievementOfMilestone" xlink:type="locator" xlink:label="sndx_PotentialMilestonePaymentsUponAchievementOfMilestone" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_UpfrontPayments" xlink:type="locator" xlink:label="sndx_UpfrontPayments" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_MinimumMember" xlink:type="locator" xlink:label="srt_MinimumMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_MaximumMember" xlink:type="locator" xlink:label="srt_MaximumMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_RangeMember" xlink:type="locator" xlink:label="srt_RangeMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_RangeAxis" xlink:type="locator" xlink:label="srt_RangeAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_BayerPharmaAgMember" xlink:type="locator" xlink:label="sndx_BayerPharmaAgMember" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_LicenseAgreementMember" xlink:type="locator" xlink:label="sndx_LicenseAgreementMember" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_EasternCooperativeOncologyGroupMember" xlink:type="locator" xlink:label="sndx_EasternCooperativeOncologyGroupMember" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_ClinicalTrialMember" xlink:type="locator" xlink:label="sndx_ClinicalTrialMember" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_AccruedMilestoneExpensesMember" xlink:type="locator" xlink:label="sndx_AccruedMilestoneExpensesMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_IncomeStatementLocationDomain" xlink:type="locator" xlink:label="us-gaap_IncomeStatementLocationDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_IncomeStatementLocationAxis" xlink:type="locator" xlink:label="us-gaap_IncomeStatementLocationAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_UCBBiopharmaMember" xlink:type="locator" xlink:label="sndx_UCBBiopharmaMember" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_UcbLicenseAgreementMember" xlink:type="locator" xlink:label="sndx_UcbLicenseAgreementMember" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_VitaePharmaceuticalsIncMember" xlink:type="locator" xlink:label="sndx_VitaePharmaceuticalsIncMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_RepurchaseAgreementCounterpartyNameDomain" xlink:type="locator" xlink:label="srt_RepurchaseAgreementCounterpartyNameDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_CounterpartyNameAxis" xlink:type="locator" xlink:label="srt_CounterpartyNameAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_AbbvieLicenseAgreementsMember" xlink:type="locator" xlink:label="sndx_AbbvieLicenseAgreementsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:type="locator" xlink:label="us-gaap_ArrangementsAndNonarrangementTransactionsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_TypeOfArrangementAxis" xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:type="locator" xlink:label="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="us-gaap_ArrangementsAndNonarrangementTransactionsMember" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:to="sndx_AbbvieLicenseAgreementsMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="srt_CounterpartyNameAxis" order="10030.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_CounterpartyNameAxis" xlink:to="srt_RepurchaseAgreementCounterpartyNameDomain" order="10200.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RepurchaseAgreementCounterpartyNameDomain" xlink:to="sndx_VitaePharmaceuticalsIncMember" order="10220.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:to="sndx_UcbLicenseAgreementMember" order="10360.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RepurchaseAgreementCounterpartyNameDomain" xlink:to="sndx_UCBBiopharmaMember" order="10540.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_IncomeStatementLocationAxis" order="10030.04" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncomeStatementLocationAxis" xlink:to="us-gaap_IncomeStatementLocationDomain" order="10700.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncomeStatementLocationDomain" xlink:to="sndx_AccruedMilestoneExpensesMember" order="10720.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:to="sndx_ClinicalTrialMember" order="10780.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RepurchaseAgreementCounterpartyNameDomain" xlink:to="sndx_EasternCooperativeOncologyGroupMember" order="10960.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:to="sndx_LicenseAgreementMember" order="11140.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RepurchaseAgreementCounterpartyNameDomain" xlink:to="sndx_BayerPharmaAgMember" order="11240.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="srt_RangeAxis" order="10030.06" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" order="11320.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" order="11340.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeMember" xlink:to="srt_MinimumMember" order="11360.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" order="11380.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="sndx_UpfrontPayments" order="11390.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="sndx_PotentialMilestonePaymentsUponAchievementOfMilestone" order="11410.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="sndx_AggregatePotentialMilestonePayable" order="11430.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="sndx_LicenseAgreementsExpirationPeriod" order="11450.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ResearchAndDevelopmentExpense" order="11470.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="sndx_MilestonePaymentDue" order="11730.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="sndx_IncreaseDecreaseInContractualObligation" order="11770.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ContractualObligation" order="11810.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="sndx_RemainingContractualObligation" order="11850.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="sndx_ContractualObligationsTerm" order="11890.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="sndx_AccruedContractualObligation" order="11930.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="sndx_UpfrontLicenseFeesPaid" order="12040.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureFairValueMeasurementsScheduleOfFairValuesOfFinancialAssetsAndLiabilitiesMeasuredAtFairValueDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureFairValueMeasurementsScheduleOfFairValuesOfFinancialAssetsAndLiabilitiesMeasuredAtFairValueDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureFairValueMeasurementsScheduleOfFairValuesOfFinancialAssetsAndLiabilitiesMeasuredAtFairValueDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AssetsFairValueDisclosure" xlink:type="locator" xlink:label="us-gaap_AssetsFairValueDisclosure" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ShortTermInvestments" xlink:type="locator" xlink:label="us-gaap_ShortTermInvestments" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CashAndCashEquivalentsFairValueDisclosure" xlink:type="locator" xlink:label="us-gaap_CashAndCashEquivalentsFairValueDisclosure" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:type="locator" xlink:label="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CarryingReportedAmountFairValueDisclosureMember" xlink:type="locator" xlink:label="us-gaap_CarryingReportedAmountFairValueDisclosureMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PortionAtFairValueFairValueDisclosureMember" xlink:type="locator" xlink:label="us-gaap_PortionAtFairValueFairValueDisclosureMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueDisclosureItemAmountsDomain" xlink:type="locator" xlink:label="us-gaap_FairValueDisclosureItemAmountsDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueByMeasurementBasisAxis" xlink:type="locator" xlink:label="us-gaap_FairValueByMeasurementBasisAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueInputsLevel3Member" xlink:type="locator" xlink:label="us-gaap_FairValueInputsLevel3Member" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueInputsLevel2Member" xlink:type="locator" xlink:label="us-gaap_FairValueInputsLevel2Member" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueInputsLevel1Member" xlink:type="locator" xlink:label="us-gaap_FairValueInputsLevel1Member" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:type="locator" xlink:label="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:type="locator" xlink:label="us-gaap_FairValueByFairValueHierarchyLevelAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:type="locator" xlink:label="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueDisclosuresAbstract" xlink:type="locator" xlink:label="us-gaap_FairValueDisclosuresAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueDisclosuresAbstract" xlink:to="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" order="10040.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_FairValueByFairValueHierarchyLevelAxis" order="10050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:to="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel1Member" order="10100.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel2Member" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel3Member" order="10140.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_FairValueByMeasurementBasisAxis" order="10050.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueDisclosureItemAmountsDomain" xlink:to="us-gaap_PortionAtFairValueFairValueDisclosureMember" order="10190.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueByMeasurementBasisAxis" xlink:to="us-gaap_FairValueDisclosureItemAmountsDomain" order="10200.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueDisclosureItemAmountsDomain" xlink:to="us-gaap_CarryingReportedAmountFairValueDisclosureMember" order="10220.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" order="10240.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_CashAndCashEquivalentsFairValueDisclosure" order="10250.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_ShortTermInvestments" order="10350.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_AssetsFairValueDisclosure" order="10450.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureFairValueMeasurementsAdditionalInformationDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureFairValueMeasurementsAdditionalInformationDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureFairValueMeasurementsAdditionalInformationDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DebtSecuritiesAvailableForSaleRealizedGainLoss" xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleRealizedGainLoss" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecurities" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CashAndCashEquivalentsFairValueDisclosure" xlink:type="locator" xlink:label="us-gaap_CashAndCashEquivalentsFairValueDisclosure" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_FairValueMeasurementsLineItems" xlink:type="locator" xlink:label="sndx_FairValueMeasurementsLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ShortTermInvestmentsMember" xlink:type="locator" xlink:label="us-gaap_ShortTermInvestmentsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_InvestmentTypeCategorizationMember" xlink:type="locator" xlink:label="us-gaap_InvestmentTypeCategorizationMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_InvestmentTypeAxis" xlink:type="locator" xlink:label="us-gaap_InvestmentTypeAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_CommercialPaperCorporateBondsAndAssetBackedSecuritiesMember" xlink:type="locator" xlink:label="sndx_CommercialPaperCorporateBondsAndAssetBackedSecuritiesMember" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_CorporateBondsAndCommercialPaperMember" xlink:type="locator" xlink:label="sndx_CorporateBondsAndCommercialPaperMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueAssetsMeasuredOnRecurringBasisUnobservableInputReconciliationByAssetClassDomain" xlink:type="locator" xlink:label="us-gaap_FairValueAssetsMeasuredOnRecurringBasisUnobservableInputReconciliationByAssetClassDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueByAssetClassAxis" xlink:type="locator" xlink:label="us-gaap_FairValueByAssetClassAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_OvernightInvestmentsMoneyMarketFundsAndCorporateBondsMember" xlink:type="locator" xlink:label="sndx_OvernightInvestmentsMoneyMarketFundsAndCorporateBondsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember" xlink:type="locator" xlink:label="us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CashAndCashEquivalentsAxis" xlink:type="locator" xlink:label="us-gaap_CashAndCashEquivalentsAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueInputsLevel2Member" xlink:type="locator" xlink:label="us-gaap_FairValueInputsLevel2Member" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueInputsLevel1Member" xlink:type="locator" xlink:label="us-gaap_FairValueInputsLevel1Member" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:type="locator" xlink:label="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:type="locator" xlink:label="us-gaap_FairValueByFairValueHierarchyLevelAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_FairValueMeasurementsTable" xlink:type="locator" xlink:label="sndx_FairValueMeasurementsTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueDisclosuresAbstract" xlink:type="locator" xlink:label="us-gaap_FairValueDisclosuresAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueDisclosuresAbstract" xlink:to="sndx_FairValueMeasurementsTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sndx_FairValueMeasurementsTable" xlink:to="us-gaap_FairValueByFairValueHierarchyLevelAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:to="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel1Member" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel2Member" order="10100.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sndx_FairValueMeasurementsTable" xlink:to="us-gaap_CashAndCashEquivalentsAxis" order="10030.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CashAndCashEquivalentsAxis" xlink:to="us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember" order="10160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember" xlink:to="sndx_OvernightInvestmentsMoneyMarketFundsAndCorporateBondsMember" order="10180.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sndx_FairValueMeasurementsTable" xlink:to="us-gaap_FairValueByAssetClassAxis" order="10030.04" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueByAssetClassAxis" xlink:to="us-gaap_FairValueAssetsMeasuredOnRecurringBasisUnobservableInputReconciliationByAssetClassDomain" order="10220.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsMeasuredOnRecurringBasisUnobservableInputReconciliationByAssetClassDomain" xlink:to="sndx_CorporateBondsAndCommercialPaperMember" order="10240.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsMeasuredOnRecurringBasisUnobservableInputReconciliationByAssetClassDomain" xlink:to="sndx_CommercialPaperCorporateBondsAndAssetBackedSecuritiesMember" order="10260.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sndx_FairValueMeasurementsTable" xlink:to="us-gaap_InvestmentTypeAxis" order="10030.06" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentTypeAxis" xlink:to="us-gaap_InvestmentTypeCategorizationMember" order="10300.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentTypeCategorizationMember" xlink:to="us-gaap_ShortTermInvestmentsMember" order="10320.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sndx_FairValueMeasurementsTable" xlink:to="sndx_FairValueMeasurementsLineItems" order="10340.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sndx_FairValueMeasurementsLineItems" xlink:to="us-gaap_CashAndCashEquivalentsFairValueDisclosure" order="10350.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sndx_FairValueMeasurementsLineItems" xlink:to="us-gaap_AvailableForSaleSecuritiesDebtSecurities" order="10430.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sndx_FairValueMeasurementsLineItems" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleRealizedGainLoss" order="10500.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureFairValueMeasurementsSummaryOfAvailableForSaleSecuritiesDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureFairValueMeasurementsSummaryOfAvailableForSaleSecuritiesDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureFairValueMeasurementsSummaryOfAvailableForSaleSecuritiesDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecurities" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:type="locator" xlink:label="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_USTreasurySecuritiesMember" xlink:type="locator" xlink:label="us-gaap_USTreasurySecuritiesMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CorporateDebtSecuritiesMember" xlink:type="locator" xlink:label="us-gaap_CorporateDebtSecuritiesMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CommercialPaperNotIncludedWithCashAndCashEquivalentsMember" xlink:type="locator" xlink:label="us-gaap_CommercialPaperNotIncludedWithCashAndCashEquivalentsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueAssetsMeasuredOnRecurringBasisUnobservableInputReconciliationByAssetClassDomain" xlink:type="locator" xlink:label="us-gaap_FairValueAssetsMeasuredOnRecurringBasisUnobservableInputReconciliationByAssetClassDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_FairValueByAssetClassAxis" xlink:type="locator" xlink:label="us-gaap_FairValueByAssetClassAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DebtSecuritiesAvailableForSaleTable" xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleTable" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_AvailableForSaleSecuritiesFairValueDisclosureAbstract" xlink:type="locator" xlink:label="sndx_AvailableForSaleSecuritiesFairValueDisclosureAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sndx_AvailableForSaleSecuritiesFairValueDisclosureAbstract" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleTable" order="10050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtSecuritiesAvailableForSaleTable" xlink:to="us-gaap_FairValueByAssetClassAxis" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueByAssetClassAxis" xlink:to="us-gaap_FairValueAssetsMeasuredOnRecurringBasisUnobservableInputReconciliationByAssetClassDomain" order="10090.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsMeasuredOnRecurringBasisUnobservableInputReconciliationByAssetClassDomain" xlink:to="us-gaap_CommercialPaperNotIncludedWithCashAndCashEquivalentsMember" order="10110.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsMeasuredOnRecurringBasisUnobservableInputReconciliationByAssetClassDomain" xlink:to="us-gaap_CorporateDebtSecuritiesMember" order="10130.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueAssetsMeasuredOnRecurringBasisUnobservableInputReconciliationByAssetClassDomain" xlink:to="us-gaap_USTreasurySecuritiesMember" order="10150.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtSecuritiesAvailableForSaleTable" xlink:to="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" order="10230.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis" order="10240.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" order="10400.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" order="10560.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleSecuritiesDebtSecurities" order="10720.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosurePrepaidExpensesAndOtherCurrentAssetsScheduleOfPrepaidExpensesAndOtherCurrentAssetsDetail" xlink:href="sndx-20210331.xsd#Role_DisclosurePrepaidExpensesAndOtherCurrentAssetsScheduleOfPrepaidExpensesAndOtherCurrentAssetsDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosurePrepaidExpensesAndOtherCurrentAssetsScheduleOfPrepaidExpensesAndOtherCurrentAssetsDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PrepaidExpenseAndOtherAssetsCurrent" xlink:type="locator" xlink:label="us-gaap_PrepaidExpenseAndOtherAssetsCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OtherPrepaidExpenseCurrent" xlink:type="locator" xlink:label="us-gaap_OtherPrepaidExpenseCurrent" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_ReimbursableCosts" xlink:type="locator" xlink:label="sndx_ReimbursableCosts" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_Supplies" xlink:type="locator" xlink:label="us-gaap_Supplies" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_PrepaidSubscriptions" xlink:type="locator" xlink:label="sndx_PrepaidSubscriptions" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_InterestReceivableCurrent" xlink:type="locator" xlink:label="us-gaap_InterestReceivableCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PrepaidInsurance" xlink:type="locator" xlink:label="us-gaap_PrepaidInsurance" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DepositsAssetsCurrent" xlink:type="locator" xlink:label="us-gaap_DepositsAssetsCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureAbstract" xlink:type="locator" xlink:label="us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureAbstract" xlink:to="us-gaap_DepositsAssetsCurrent" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureAbstract" xlink:to="us-gaap_PrepaidInsurance" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureAbstract" xlink:to="us-gaap_InterestReceivableCurrent" order="10160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureAbstract" xlink:to="sndx_PrepaidSubscriptions" order="10200.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureAbstract" xlink:to="us-gaap_Supplies" order="10240.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureAbstract" xlink:to="sndx_ReimbursableCosts" order="10280.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureAbstract" xlink:to="us-gaap_OtherPrepaidExpenseCurrent" order="10320.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DeferredCostsCapitalizedPrepaidAndOtherAssetsDisclosureAbstract" xlink:to="us-gaap_PrepaidExpenseAndOtherAssetsCurrent" order="10360.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureAccruedExpensesAndOtherCurrentLiabilitiesScheduleOfAccruedExpensesAndOtherCurrentLiabilitiesDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureAccruedExpensesAndOtherCurrentLiabilitiesScheduleOfAccruedExpensesAndOtherCurrentLiabilitiesDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureAccruedExpensesAndOtherCurrentLiabilitiesScheduleOfAccruedExpensesAndOtherCurrentLiabilitiesDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AccruedLiabilitiesAndOtherLiabilities" xlink:type="locator" xlink:label="us-gaap_AccruedLiabilitiesAndOtherLiabilities" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OtherAccruedLiabilitiesCurrent" xlink:type="locator" xlink:label="us-gaap_OtherAccruedLiabilitiesCurrent" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_AccruedInterestPayable" xlink:type="locator" xlink:label="sndx_AccruedInterestPayable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AccruedProfessionalFeesCurrent" xlink:type="locator" xlink:label="us-gaap_AccruedProfessionalFeesCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EmployeeRelatedLiabilitiesCurrent" xlink:type="locator" xlink:label="us-gaap_EmployeeRelatedLiabilitiesCurrent" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_AccruedClinicalCostsCurrent" xlink:type="locator" xlink:label="sndx_AccruedClinicalCostsCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PayablesAndAccrualsAbstract" xlink:type="locator" xlink:label="us-gaap_PayablesAndAccrualsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PayablesAndAccrualsAbstract" xlink:to="sndx_AccruedClinicalCostsCurrent" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PayablesAndAccrualsAbstract" xlink:to="us-gaap_EmployeeRelatedLiabilitiesCurrent" order="10100.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PayablesAndAccrualsAbstract" xlink:to="us-gaap_AccruedProfessionalFeesCurrent" order="10140.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PayablesAndAccrualsAbstract" xlink:to="sndx_AccruedInterestPayable" order="10180.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PayablesAndAccrualsAbstract" xlink:to="us-gaap_OtherAccruedLiabilitiesCurrent" order="10220.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PayablesAndAccrualsAbstract" xlink:to="us-gaap_AccruedLiabilitiesAndOtherLiabilities" order="10260.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockBasedCompensationAdditionalInformationDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureStockBasedCompensationAdditionalInformationDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockBasedCompensationAdditionalInformationDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedWeightedAverageGrantDateFairValue" xlink:type="locator" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedWeightedAverageGrantDateFairValue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedNumberOfShares" xlink:type="locator" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedNumberOfShares" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedOptionsForfeitedWeightedAverageGrantDateFairValue" xlink:type="locator" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedOptionsForfeitedWeightedAverageGrantDateFairValue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedPeriodForRecognition1" xlink:type="locator" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedPeriodForRecognition1" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions" xlink:type="locator" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ProceedsFromStockOptionsExercised" xlink:type="locator" xlink:label="us-gaap_ProceedsFromStockOptionsExercised" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingNumber" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingNumber" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_EmployeeServiceShareBasedCompensationRecognizedStockOptionsCancelled" xlink:type="locator" xlink:label="sndx_EmployeeServiceShareBasedCompensationRecognizedStockOptionsCancelled" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_EmployeeServiceShareBasedCompensationRecognizedStockOptionsNotMet" xlink:type="locator" xlink:label="sndx_EmployeeServiceShareBasedCompensationRecognizedStockOptionsNotMet" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_EmployeeServiceShareBasedCompensationRecognizedStockOptions" xlink:type="locator" xlink:label="sndx_EmployeeServiceShareBasedCompensationRecognizedStockOptions" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_ShareBasedCompensationArrangementByShareBasedPaymentAwardStockOptionGrantDateFairValue" xlink:type="locator" xlink:label="sndx_ShareBasedCompensationArrangementByShareBasedPaymentAwardStockOptionGrantDateFairValue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriod" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriod" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CommonStockCapitalSharesReservedForFutureIssuance" xlink:type="locator" xlink:label="us-gaap_CommonStockCapitalSharesReservedForFutureIssuance" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RestrictedStockUnitsRSUMember" xlink:type="locator" xlink:label="us-gaap_RestrictedStockUnitsRSUMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AwardTypeAxis" xlink:type="locator" xlink:label="us-gaap_AwardTypeAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_TwoThousandSevenAndTwoThousandFifteenStockIncentivePlanMember" xlink:type="locator" xlink:label="sndx_TwoThousandSevenAndTwoThousandFifteenStockIncentivePlanMember" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_EmployeesMember" xlink:type="locator" xlink:label="sndx_EmployeesMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_TitleOfIndividualWithRelationshipToEntityDomain" xlink:type="locator" xlink:label="srt_TitleOfIndividualWithRelationshipToEntityDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_TitleOfIndividualAxis" xlink:type="locator" xlink:label="srt_TitleOfIndividualAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_TwoThousandAndSevenStockIncentivePlanMember" xlink:type="locator" xlink:label="sndx_TwoThousandAndSevenStockIncentivePlanMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_MinimumMember" xlink:type="locator" xlink:label="srt_MinimumMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_MaximumMember" xlink:type="locator" xlink:label="srt_MaximumMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_RangeMember" xlink:type="locator" xlink:label="srt_RangeMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_RangeAxis" xlink:type="locator" xlink:label="srt_RangeAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_TwoThousandFifteenOmnibusIncentivePlanMember" xlink:type="locator" xlink:label="sndx_TwoThousandFifteenOmnibusIncentivePlanMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PlanNameDomain" xlink:type="locator" xlink:label="us-gaap_PlanNameDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PlanNameAxis" xlink:type="locator" xlink:label="us-gaap_PlanNameAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:type="locator" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_PlanNameAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PlanNameDomain" xlink:to="sndx_TwoThousandFifteenOmnibusIncentivePlanMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="srt_RangeAxis" order="10030.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" order="10140.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" order="10160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeMember" xlink:to="srt_MinimumMember" order="10180.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PlanNameDomain" xlink:to="sndx_TwoThousandAndSevenStockIncentivePlanMember" order="10240.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="srt_TitleOfIndividualAxis" order="10030.04" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_TitleOfIndividualAxis" xlink:to="srt_TitleOfIndividualWithRelationshipToEntityDomain" order="10380.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_TitleOfIndividualWithRelationshipToEntityDomain" xlink:to="sndx_EmployeesMember" order="10400.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PlanNameDomain" xlink:to="sndx_TwoThousandSevenAndTwoThousandFifteenStockIncentivePlanMember" order="10600.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_AwardTypeAxis" order="10030.06" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" order="10660.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_RestrictedStockUnitsRSUMember" order="10680.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" order="10800.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_CommonStockCapitalSharesReservedForFutureIssuance" order="10810.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriod" order="10880.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sndx_ShareBasedCompensationArrangementByShareBasedPaymentAwardStockOptionGrantDateFairValue" order="10900.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" order="10920.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sndx_EmployeeServiceShareBasedCompensationRecognizedStockOptions" order="11020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sndx_EmployeeServiceShareBasedCompensationRecognizedStockOptionsNotMet" order="11080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sndx_EmployeeServiceShareBasedCompensationRecognizedStockOptionsCancelled" order="11140.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross" order="11200.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingNumber" order="11260.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" order="11350.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ProceedsFromStockOptionsExercised" order="11390.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions" order="11460.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedPeriodForRecognition1" order="11480.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1" order="11550.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedOptionsForfeitedWeightedAverageGrantDateFairValue" order="11590.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedNumberOfShares" order="11610.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedWeightedAverageGrantDateFairValue" order="11630.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockBasedCompensationShareBasedCompensationExpenseRelatedToIssuanceOfStockOptionAwardsToEmployeesAndNonEmployeesRelatedToEmployeeStockPurchasePlanDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureStockBasedCompensationShareBasedCompensationExpenseRelatedToIssuanceOfStockOptionAwardsToEmployeesAndNonEmployeesRelatedToEmployeeStockPurchasePlanDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockBasedCompensationShareBasedCompensationExpenseRelatedToIssuanceOfStockOptionAwardsToEmployeesAndNonEmployeesRelatedToEmployeeStockPurchasePlanDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AllocatedShareBasedCompensationExpense" xlink:type="locator" xlink:label="us-gaap_AllocatedShareBasedCompensationExpense" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_GeneralAndAdministrativeExpenseMember" xlink:type="locator" xlink:label="us-gaap_GeneralAndAdministrativeExpenseMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ResearchAndDevelopmentExpenseMember" xlink:type="locator" xlink:label="us-gaap_ResearchAndDevelopmentExpenseMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_IncomeStatementLocationDomain" xlink:type="locator" xlink:label="us-gaap_IncomeStatementLocationDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_IncomeStatementLocationAxis" xlink:type="locator" xlink:label="us-gaap_IncomeStatementLocationAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AccountingPoliciesAbstract" xlink:type="locator" xlink:label="us-gaap_AccountingPoliciesAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_IncomeStatementLocationAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncomeStatementLocationAxis" xlink:to="us-gaap_IncomeStatementLocationDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncomeStatementLocationDomain" xlink:to="us-gaap_ResearchAndDevelopmentExpenseMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncomeStatementLocationDomain" xlink:to="us-gaap_GeneralAndAdministrativeExpenseMember" order="10100.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_AllocatedShareBasedCompensationExpense" order="10130.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockBasedCompensationCompensationExpenseByTypeOfAwardDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureStockBasedCompensationCompensationExpenseByTypeOfAwardDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockBasedCompensationCompensationExpenseByTypeOfAwardDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AllocatedShareBasedCompensationExpense" xlink:type="locator" xlink:label="us-gaap_AllocatedShareBasedCompensationExpense" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RestrictedStockUnitsRSUMember" xlink:type="locator" xlink:label="us-gaap_RestrictedStockUnitsRSUMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EmployeeStockOptionMember" xlink:type="locator" xlink:label="us-gaap_EmployeeStockOptionMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AwardTypeAxis" xlink:type="locator" xlink:label="us-gaap_AwardTypeAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_EmployeeStockPurchasePlanMember" xlink:type="locator" xlink:label="sndx_EmployeeStockPurchasePlanMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PlanNameDomain" xlink:type="locator" xlink:label="us-gaap_PlanNameDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PlanNameAxis" xlink:type="locator" xlink:label="us-gaap_PlanNameAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AccountingPoliciesAbstract" xlink:type="locator" xlink:label="us-gaap_AccountingPoliciesAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_PlanNameAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PlanNameDomain" xlink:to="sndx_EmployeeStockPurchasePlanMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_AwardTypeAxis" order="10030.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_EmployeeStockOptionMember" order="10140.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_RestrictedStockUnitsRSUMember" order="10160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" order="10180.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_AllocatedShareBasedCompensationExpense" order="10190.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureLoanPayableAdditionalInformationDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureLoanPayableAdditionalInformationDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureLoanPayableAdditionalInformationDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_InterestExpense" xlink:type="locator" xlink:label="us-gaap_InterestExpense" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_AdditionalDefaultInterestRate" xlink:type="locator" xlink:label="sndx_AdditionalDefaultInterestRate" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_LineOfCreditFacilityCashCovenantDeferred" xlink:type="locator" xlink:label="sndx_LineOfCreditFacilityCashCovenantDeferred" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_LineOfCreditFacilityMinimumCashCovenant" xlink:type="locator" xlink:label="sndx_LineOfCreditFacilityMinimumCashCovenant" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_PercentageOfRepaymentOnAggregatePrincipalAmountOfTermLoanAdvances" xlink:type="locator" xlink:label="sndx_PercentageOfRepaymentOnAggregatePrincipalAmountOfTermLoanAdvances" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_PaymentOfFacilityCharges" xlink:type="locator" xlink:label="sndx_PaymentOfFacilityCharges" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_PercentageOfPrepaymentPremiumOfPrincipalAmountOutstandingThereafter" xlink:type="locator" xlink:label="sndx_PercentageOfPrepaymentPremiumOfPrincipalAmountOutstandingThereafter" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_PercentageOfPrepaymentPremiumOfPrincipalAmountOutstandingInSecondYear" xlink:type="locator" xlink:label="sndx_PercentageOfPrepaymentPremiumOfPrincipalAmountOutstandingInSecondYear" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_PercentageOfPrepaymentPremiumOfPrincipalAmountOutstandingInFirstYear" xlink:type="locator" xlink:label="sndx_PercentageOfPrepaymentPremiumOfPrincipalAmountOutstandingInFirstYear" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DebtInstrumentMaturityDate" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentMaturityDate" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DebtInstrumentInterestRateEffectivePercentage" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateEffectivePercentage" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DebtInstrumentBasisSpreadOnVariableRate1" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentBasisSpreadOnVariableRate1" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DebtInstrumentInterestRateStatedPercentage" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateStatedPercentage" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LineOfCreditFacilityInterestRateDescription" xlink:type="locator" xlink:label="us-gaap_LineOfCreditFacilityInterestRateDescription" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_LineOfCreditFacilityElectedNotToDraw" xlink:type="locator" xlink:label="sndx_LineOfCreditFacilityElectedNotToDraw" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LineOfCreditFacilityMaximumBorrowingCapacity" xlink:type="locator" xlink:label="us-gaap_LineOfCreditFacilityMaximumBorrowingCapacity" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DebtInstrumentLineItems" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PrimeRateMember" xlink:type="locator" xlink:label="us-gaap_PrimeRateMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_VariableRateDomain" xlink:type="locator" xlink:label="us-gaap_VariableRateDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_VariableRateAxis" xlink:type="locator" xlink:label="us-gaap_VariableRateAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_MaximumMember" xlink:type="locator" xlink:label="srt_MaximumMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_MinimumMember" xlink:type="locator" xlink:label="srt_MinimumMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_RangeMember" xlink:type="locator" xlink:label="srt_RangeMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_RangeAxis" xlink:type="locator" xlink:label="srt_RangeAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_AdditionalTermLoanMember" xlink:type="locator" xlink:label="sndx_AdditionalTermLoanMember" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_TermLoanMember" xlink:type="locator" xlink:label="sndx_TermLoanMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DebtInstrumentNameDomain" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentNameDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DebtInstrumentAxis" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_LoanAndSecurityAgreementMember" xlink:type="locator" xlink:label="sndx_LoanAndSecurityAgreementMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CreditFacilityDomain" xlink:type="locator" xlink:label="us-gaap_CreditFacilityDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CreditFacilityAxis" xlink:type="locator" xlink:label="us-gaap_CreditFacilityAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_HerculesCapitalIncMember" xlink:type="locator" xlink:label="sndx_HerculesCapitalIncMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LineOfCreditFacilityLenderDomain" xlink:type="locator" xlink:label="us-gaap_LineOfCreditFacilityLenderDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LineOfCreditFacilityAxis" xlink:type="locator" xlink:label="us-gaap_LineOfCreditFacilityAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DebtInstrumentTable" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DebtDisclosureAbstract" xlink:type="locator" xlink:label="us-gaap_DebtDisclosureAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtDisclosureAbstract" xlink:to="us-gaap_DebtInstrumentTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_LineOfCreditFacilityAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LineOfCreditFacilityAxis" xlink:to="us-gaap_LineOfCreditFacilityLenderDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LineOfCreditFacilityLenderDomain" xlink:to="sndx_HerculesCapitalIncMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_CreditFacilityAxis" order="10030.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CreditFacilityAxis" xlink:to="us-gaap_CreditFacilityDomain" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CreditFacilityDomain" xlink:to="sndx_LoanAndSecurityAgreementMember" order="10140.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_DebtInstrumentAxis" order="10030.04" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="us-gaap_DebtInstrumentNameDomain" order="10180.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentNameDomain" xlink:to="sndx_TermLoanMember" order="10200.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentNameDomain" xlink:to="sndx_AdditionalTermLoanMember" order="10220.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="srt_RangeAxis" order="10030.06" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" order="10280.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeMember" xlink:to="srt_MinimumMember" order="10300.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" order="10320.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_VariableRateAxis" order="10030.08" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_VariableRateAxis" xlink:to="us-gaap_VariableRateDomain" order="10360.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_VariableRateDomain" xlink:to="us-gaap_PrimeRateMember" order="10380.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_DebtInstrumentLineItems" order="10840.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_LineOfCreditFacilityMaximumBorrowingCapacity" order="10850.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="sndx_LineOfCreditFacilityElectedNotToDraw" order="10910.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_LineOfCreditFacilityInterestRateDescription" order="10930.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentInterestRateStatedPercentage" order="10950.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentBasisSpreadOnVariableRate1" order="10970.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentInterestRateEffectivePercentage" order="10990.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentMaturityDate" order="11040.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="sndx_PercentageOfPrepaymentPremiumOfPrincipalAmountOutstandingInFirstYear" order="11060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="sndx_PercentageOfPrepaymentPremiumOfPrincipalAmountOutstandingInSecondYear" order="11080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="sndx_PercentageOfPrepaymentPremiumOfPrincipalAmountOutstandingThereafter" order="11100.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="sndx_PaymentOfFacilityCharges" order="11120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="sndx_PercentageOfRepaymentOnAggregatePrincipalAmountOfTermLoanAdvances" order="11140.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="sndx_LineOfCreditFacilityMinimumCashCovenant" order="11190.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="sndx_LineOfCreditFacilityCashCovenantDeferred" order="11210.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="sndx_AdditionalDefaultInterestRate" order="11230.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_InterestExpense" order="11280.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureLoanPayableSummaryOfMaturitiesOfPrincipalObligationsUnderLongTermDebtDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureLoanPayableSummaryOfMaturitiesOfPrincipalObligationsUnderLongTermDebtDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureLoanPayableSummaryOfMaturitiesOfPrincipalObligationsUnderLongTermDebtDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LongTermLoansPayable" xlink:type="locator" xlink:label="us-gaap_LongTermLoansPayable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LoansPayableCurrent" xlink:type="locator" xlink:label="us-gaap_LoansPayableCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LoansPayable" xlink:type="locator" xlink:label="us-gaap_LoansPayable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_UnamortizedDebtIssuanceExpense" xlink:type="locator" xlink:label="us-gaap_UnamortizedDebtIssuanceExpense" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_AmortizedLossesReacquiredDebtNoncurrent" xlink:type="locator" xlink:label="sndx_AmortizedLossesReacquiredDebtNoncurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DebtInstrumentCarryingAmount" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentCarryingAmount" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalInYearTwo" xlink:type="locator" xlink:label="us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalInYearTwo" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalInNextTwelveMonths" xlink:type="locator" xlink:label="us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalInNextTwelveMonths" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalRemainderOfFiscalYear" xlink:type="locator" xlink:label="us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalRemainderOfFiscalYear" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DebtDisclosureAbstract" xlink:type="locator" xlink:label="us-gaap_DebtDisclosureAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtDisclosureAbstract" xlink:to="us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalRemainderOfFiscalYear" order="10070.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtDisclosureAbstract" xlink:to="us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalInNextTwelveMonths" order="10090.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtDisclosureAbstract" xlink:to="us-gaap_LongTermDebtMaturitiesRepaymentsOfPrincipalInYearTwo" order="10110.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtDisclosureAbstract" xlink:to="us-gaap_DebtInstrumentCarryingAmount" order="10130.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtDisclosureAbstract" xlink:to="sndx_AmortizedLossesReacquiredDebtNoncurrent" order="10150.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtDisclosureAbstract" xlink:to="us-gaap_UnamortizedDebtIssuanceExpense" order="10170.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtDisclosureAbstract" xlink:to="us-gaap_LoansPayable" order="10190.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtDisclosureAbstract" xlink:to="us-gaap_LoansPayableCurrent" order="10210.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtDisclosureAbstract" xlink:to="us-gaap_LongTermLoansPayable" order="10230.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/positiveLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockholdersEquitySummaryOfChangesInStockholdersEquityDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureStockholdersEquitySummaryOfChangesInStockholdersEquityDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockholdersEquitySummaryOfChangesInStockholdersEquityDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_SharesOutstanding" xlink:type="locator" xlink:label="us-gaap_SharesOutstanding_li0l2" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StockholdersEquity" xlink:type="locator" xlink:label="us-gaap_StockholdersEquity_li0l2" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NetIncomeLoss" xlink:type="locator" xlink:label="us-gaap_NetIncomeLoss" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StockIssuedDuringPeriodValueStockOptionsExercised" xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodValueStockOptionsExercised" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AdjustmentToAdditionalPaidInCapitalIncomeTaxEffectFromShareBasedCompensationNet" xlink:type="locator" xlink:label="us-gaap_AdjustmentToAdditionalPaidInCapitalIncomeTaxEffectFromShareBasedCompensationNet" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_PrefundedWarrantExchangeShares" xlink:type="locator" xlink:label="sndx_PrefundedWarrantExchangeShares" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" xlink:type="locator" xlink:label="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_AdjustmentsToAdditionalPaidInCapitalRepricingWarrants" xlink:type="locator" xlink:label="sndx_AdjustmentsToAdditionalPaidInCapitalRepricingWarrants" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_AdjustmentsToAdditionalPaidInCapitalDeemedDividendFromRepricingWarrants" xlink:type="locator" xlink:label="sndx_AdjustmentsToAdditionalPaidInCapitalDeemedDividendFromRepricingWarrants" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_StockIssuedDuringPeriodValuePreFundedCommonStockWarrantsFromDirectOffering" xlink:type="locator" xlink:label="sndx_StockIssuedDuringPeriodValuePreFundedCommonStockWarrantsFromDirectOffering" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_StockIssuedDuringPeriodSharesDirectOffering" xlink:type="locator" xlink:label="sndx_StockIssuedDuringPeriodSharesDirectOffering" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_StockIssuedDuringPeriodValueDirectOffering" xlink:type="locator" xlink:label="sndx_StockIssuedDuringPeriodValueDirectOffering" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue" xlink:type="locator" xlink:label="us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesEmployeeStockPurchasePlans" xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodSharesEmployeeStockPurchasePlans" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_SharesOutstanding" xlink:type="locator" xlink:label="us-gaap_SharesOutstanding" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StockholdersEquity" xlink:type="locator" xlink:label="us-gaap_StockholdersEquity" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ClassOfStockLineItems" xlink:type="locator" xlink:label="us-gaap_ClassOfStockLineItems" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_SeriesOneAndTwoMember" xlink:type="locator" xlink:label="sndx_SeriesOneAndTwoMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ClassOfWarrantOrRightDomain" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ClassOfWarrantOrRightAxis" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RetainedEarningsMember" xlink:type="locator" xlink:label="us-gaap_RetainedEarningsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AccumulatedOtherComprehensiveIncomeMember" xlink:type="locator" xlink:label="us-gaap_AccumulatedOtherComprehensiveIncomeMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AdditionalPaidInCapitalMember" xlink:type="locator" xlink:label="us-gaap_AdditionalPaidInCapitalMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CommonStockMember" xlink:type="locator" xlink:label="us-gaap_CommonStockMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EquityComponentDomain" xlink:type="locator" xlink:label="us-gaap_EquityComponentDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StatementEquityComponentsAxis" xlink:type="locator" xlink:label="us-gaap_StatementEquityComponentsAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfStockByClassTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfStockByClassTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EquityAbstract" xlink:type="locator" xlink:label="us-gaap_EquityAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityAbstract" xlink:to="us-gaap_ScheduleOfStockByClassTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_StatementEquityComponentsAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_CommonStockMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_AdditionalPaidInCapitalMember" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_AccumulatedOtherComprehensiveIncomeMember" order="10140.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_RetainedEarningsMember" order="10160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_ClassOfWarrantOrRightAxis" order="10030.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfWarrantOrRightAxis" xlink:to="us-gaap_ClassOfWarrantOrRightDomain" order="10340.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfWarrantOrRightDomain" xlink:to="sndx_SeriesOneAndTwoMember" order="10360.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_ClassOfStockLineItems" order="10400.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_StockholdersEquity" order="10410.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_SharesOutstanding" order="10430.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesEmployeeStockPurchasePlans" order="10550.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue" order="10690.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sndx_StockIssuedDuringPeriodValueDirectOffering" order="10830.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sndx_StockIssuedDuringPeriodSharesDirectOffering" order="10850.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sndx_StockIssuedDuringPeriodValuePreFundedCommonStockWarrantsFromDirectOffering" order="10970.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sndx_AdjustmentsToAdditionalPaidInCapitalDeemedDividendFromRepricingWarrants" order="11110.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sndx_AdjustmentsToAdditionalPaidInCapitalRepricingWarrants" order="11250.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" order="11390.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sndx_PrefundedWarrantExchangeShares" order="11530.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_AdjustmentToAdditionalPaidInCapitalIncomeTaxEffectFromShareBasedCompensationNet" order="11670.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodValueStockOptionsExercised" order="11810.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" order="11830.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_NetIncomeLoss" order="11950.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_StockholdersEquity_li0l2" order="12090.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_SharesOutstanding_li0l2" order="12110.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockholdersEquitySummaryOfChangesInStockholdersEquityParentheticalDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureStockholdersEquitySummaryOfChangesInStockholdersEquityParentheticalDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockholdersEquitySummaryOfChangesInStockholdersEquityParentheticalDetail">
    <link:loc xlink:href="sndx-20210331.xsd#sndx_StockIssuedDuringPeriodValuePreFundedCommonStockWarrantOfferingExpenses" xlink:type="locator" xlink:label="sndx_StockIssuedDuringPeriodValuePreFundedCommonStockWarrantOfferingExpenses" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_StockIssuedDuringPeriodValueOfferingExpenses" xlink:type="locator" xlink:label="sndx_StockIssuedDuringPeriodValueOfferingExpenses" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EquityAbstract" xlink:type="locator" xlink:label="us-gaap_EquityAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityAbstract" xlink:to="sndx_StockIssuedDuringPeriodValueOfferingExpenses" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityAbstract" xlink:to="sndx_StockIssuedDuringPeriodValuePreFundedCommonStockWarrantOfferingExpenses" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockholdersEquityAdditionalInformationDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureStockholdersEquityAdditionalInformationDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockholdersEquityAdditionalInformationDetail">
    <link:loc xlink:href="sndx-20210331.xsd#sndx_AdjustmentsToAdditionalPaidInCapitalRepricingWarrants" xlink:type="locator" xlink:label="sndx_AdjustmentsToAdditionalPaidInCapitalRepricingWarrants" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_WarrantsAndRightsOutstandingTerm" xlink:type="locator" xlink:label="us-gaap_WarrantsAndRightsOutstandingTerm" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_WarrantsAndRightsOutstandingMeasurementInput" xlink:type="locator" xlink:label="us-gaap_WarrantsAndRightsOutstandingMeasurementInput" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_FairValueOfWarrants" xlink:type="locator" xlink:label="sndx_FairValueOfWarrants" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_MaximumBeneficialOwnershipLimitationPercentage" xlink:type="locator" xlink:label="sndx_MaximumBeneficialOwnershipLimitationPercentage" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_ExerciseOfWarrantsLowerLimitAfterExerciseAsPercentageOfCommonStock" xlink:type="locator" xlink:label="sndx_ExerciseOfWarrantsLowerLimitAfterExerciseAsPercentageOfCommonStock" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_MaximumPeriodAllowedToIncreaseBeneficialOwnershipLimitationAfterNotice" xlink:type="locator" xlink:label="sndx_MaximumPeriodAllowedToIncreaseBeneficialOwnershipLimitationAfterNotice" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_WarrantsExercisedPeriod" xlink:type="locator" xlink:label="sndx_WarrantsExercisedPeriod" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_OfferingCost" xlink:type="locator" xlink:label="sndx_OfferingCost" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_GrossProceedsFromOffering" xlink:type="locator" xlink:label="sndx_GrossProceedsFromOffering" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_OfferingPricePerShare" xlink:type="locator" xlink:label="sndx_OfferingPricePerShare" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_ClassOfWarrantOrRightTerm" xlink:type="locator" xlink:label="sndx_ClassOfWarrantOrRightTerm" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_NumberOfSeriesOfWarrants" xlink:type="locator" xlink:label="sndx_NumberOfSeriesOfWarrants" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues" xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodSharesNewIssues" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ProceedsFromIssuanceOfCommonStock" xlink:type="locator" xlink:label="us-gaap_ProceedsFromIssuanceOfCommonStock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ClassOfStockLineItems" xlink:type="locator" xlink:label="us-gaap_ClassOfStockLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_MinimumMember" xlink:type="locator" xlink:label="srt_MinimumMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_MaximumMember" xlink:type="locator" xlink:label="srt_MaximumMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_RangeMember" xlink:type="locator" xlink:label="srt_RangeMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2020/elts/srt-2020-01-31.xsd#srt_RangeAxis" xlink:type="locator" xlink:label="srt_RangeAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_MeasurementInputOptionVolatilityMember" xlink:type="locator" xlink:label="us-gaap_MeasurementInputOptionVolatilityMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_MeasurementInputTypeDomain" xlink:type="locator" xlink:label="us-gaap_MeasurementInputTypeDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_MeasurementInputTypeAxis" xlink:type="locator" xlink:label="us-gaap_MeasurementInputTypeAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_SeriesOneAndSeriesTwoWarrantsMember" xlink:type="locator" xlink:label="sndx_SeriesOneAndSeriesTwoWarrantsMember" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_SeriesTwoWarrantsMember" xlink:type="locator" xlink:label="sndx_SeriesTwoWarrantsMember" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_SeriesOneWarrantsMember" xlink:type="locator" xlink:label="sndx_SeriesOneWarrantsMember" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_SeriesWarrantsMember" xlink:type="locator" xlink:label="sndx_SeriesWarrantsMember" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_PreFundedWarrantsMember" xlink:type="locator" xlink:label="sndx_PreFundedWarrantsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CommonStockMember" xlink:type="locator" xlink:label="us-gaap_CommonStockMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EquityComponentDomain" xlink:type="locator" xlink:label="us-gaap_EquityComponentDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StatementEquityComponentsAxis" xlink:type="locator" xlink:label="us-gaap_StatementEquityComponentsAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_AtTheMarketEquityOfferingSalesAgreementMember" xlink:type="locator" xlink:label="sndx_AtTheMarketEquityOfferingSalesAgreementMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RelatedPartyTransactionDomain" xlink:type="locator" xlink:label="us-gaap_RelatedPartyTransactionDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RelatedPartyTransactionAxis" xlink:type="locator" xlink:label="us-gaap_RelatedPartyTransactionAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_CowenAndCompanyLLCMember" xlink:type="locator" xlink:label="sndx_CowenAndCompanyLLCMember" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_EntityDomain" xlink:type="locator" xlink:label="dei_EntityDomain" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2020/dei-2020-01-31.xsd#dei_LegalEntityAxis" xlink:type="locator" xlink:label="dei_LegalEntityAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfStockByClassTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfStockByClassTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EquityAbstract" xlink:type="locator" xlink:label="us-gaap_EquityAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityAbstract" xlink:to="us-gaap_ScheduleOfStockByClassTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="dei_LegalEntityAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_LegalEntityAxis" xlink:to="dei_EntityDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_EntityDomain" xlink:to="sndx_CowenAndCompanyLLCMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_RelatedPartyTransactionAxis" order="10030.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RelatedPartyTransactionAxis" xlink:to="us-gaap_RelatedPartyTransactionDomain" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RelatedPartyTransactionDomain" xlink:to="sndx_AtTheMarketEquityOfferingSalesAgreementMember" order="10140.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_StatementEquityComponentsAxis" order="10030.04" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" order="10320.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_CommonStockMember" order="10340.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="sndx_PreFundedWarrantsMember" order="10360.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="sndx_SeriesWarrantsMember" order="10380.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="sndx_SeriesOneWarrantsMember" order="10520.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="sndx_SeriesTwoWarrantsMember" order="10540.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="sndx_SeriesOneAndSeriesTwoWarrantsMember" order="10580.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_MeasurementInputTypeAxis" order="10030.06" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_MeasurementInputTypeAxis" xlink:to="us-gaap_MeasurementInputTypeDomain" order="10800.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_MeasurementInputTypeDomain" xlink:to="us-gaap_MeasurementInputOptionVolatilityMember" order="10820.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="srt_RangeAxis" order="10030.08" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" order="11040.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" order="11060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeMember" xlink:to="srt_MinimumMember" order="11080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_ClassOfStockLineItems" order="11200.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_ProceedsFromIssuanceOfCommonStock" order="11210.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/positiveTerseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesNewIssues" order="11230.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sndx_NumberOfSeriesOfWarrants" order="11350.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" order="11370.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" order="11410.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sndx_ClassOfWarrantOrRightTerm" order="11430.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sndx_OfferingPricePerShare" order="11450.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sndx_GrossProceedsFromOffering" order="11490.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sndx_OfferingCost" order="11510.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sndx_WarrantsExercisedPeriod" order="11620.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sndx_MaximumPeriodAllowedToIncreaseBeneficialOwnershipLimitationAfterNotice" order="11670.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sndx_ExerciseOfWarrantsLowerLimitAfterExerciseAsPercentageOfCommonStock" order="11690.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sndx_MaximumBeneficialOwnershipLimitationPercentage" order="11710.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sndx_FairValueOfWarrants" order="11780.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_WarrantsAndRightsOutstandingMeasurementInput" order="11800.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_WarrantsAndRightsOutstandingTerm" order="11820.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sndx_AdjustmentsToAdditionalPaidInCapitalRepricingWarrants" order="12030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockholdersEquityScheduleOfCommonStockReservedForFutureIssuanceDetail" xlink:href="sndx-20210331.xsd#Role_DisclosureStockholdersEquityScheduleOfCommonStockReservedForFutureIssuanceDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.syndax.com/20210331/taxonomy/role/DisclosureStockholdersEquityScheduleOfCommonStockReservedForFutureIssuanceDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CommonStockCapitalSharesReservedForFutureIssuance" xlink:type="locator" xlink:label="us-gaap_CommonStockCapitalSharesReservedForFutureIssuance" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ClassOfStockLineItems" xlink:type="locator" xlink:label="us-gaap_ClassOfStockLineItems" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_PreFundedWarrantsMember" xlink:type="locator" xlink:label="sndx_PreFundedWarrantsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EquityComponentDomain" xlink:type="locator" xlink:label="us-gaap_EquityComponentDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StatementEquityComponentsAxis" xlink:type="locator" xlink:label="us-gaap_StatementEquityComponentsAxis" />
    <link:loc xlink:href="sndx-20210331.xsd#sndx_EmployeeStockPurchasePlanMember" xlink:type="locator" xlink:label="sndx_EmployeeStockPurchasePlanMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EmployeeStockOptionMember" xlink:type="locator" xlink:label="us-gaap_EmployeeStockOptionMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AwardTypeAxis" xlink:type="locator" xlink:label="us-gaap_AwardTypeAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ScheduleOfStockByClassTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfStockByClassTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_EquityAbstract" xlink:type="locator" xlink:label="us-gaap_EquityAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityAbstract" xlink:to="us-gaap_ScheduleOfStockByClassTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_AwardTypeAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_EmployeeStockOptionMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="sndx_EmployeeStockPurchasePlanMember" order="10100.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_StatementEquityComponentsAxis" order="10030.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" order="10140.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="sndx_PreFundedWarrantsMember" order="10160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_ClassOfStockLineItems" order="10180.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_CommonStockCapitalSharesReservedForFutureIssuance" order="10190.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/positiveTerseLabel" />
  </link:presentationLink>
</link:linkbase>
