<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2020-05-15</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001042074</issuerCik>
        <issuerName>CymaBay Therapeutics, Inc.</issuerName>
        <issuerTradingSymbol>CBAY</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001252524</rptOwnerCik>
            <rptOwnerName>EMSTER KURT VON</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O CYMABAY THERAPEUTICS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>7575 GATEWAY BOULEVARD, SUITE 110</rptOwnerStreet2>
            <rptOwnerCity>NEWARK</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94560</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>4.05</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2020-05-15</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>49245</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2030-05-14</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>49245</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>49245</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The shares subject to the option shall vest in 12 equal monthly installments commencing on January 31, 2020, subject to the Reporting Person's continuous service to the Issuer as of each such date.</footnote>
    </footnotes>

    <remarks>On May 19, 2020, the Reporting Person filed a Form 4 under CIK 0001588856 (the &quot;Prior CIK&quot;). The Reporting Person was inadvertently issued two sets of EDGAR access codes. This Form 4 is being filed using the Reporting Person's current CIK reporting the same grant as reported in the May 19, 2020 filing using the Prior CIK, and does not reflect the grant of an additional option.</remarks>

    <ownerSignature>
        <signatureName>/s/ Sujal Shah, Attorney-in-Fact for Kurt von Emster</signatureName>
        <signatureDate>2020-06-23</signatureDate>
    </ownerSignature>
</ownershipDocument>
