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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2016-06-16</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001503802</issuerCik>
        <issuerName>Karyopharm Therapeutics Inc.</issuerName>
        <issuerTradingSymbol>KPTI</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001270734</rptOwnerCik>
            <rptOwnerName>PAKIANATHAN DEEPIKA</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O DELPHI VENTURES, 160 BOVET RD.</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 408</rptOwnerStreet2>
            <rptOwnerCity>SAN MATEO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94402</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Nonstatutory Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>8.06</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2016-06-16</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>10000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2026-06-15</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>10000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>10000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">This option vests as to 100% of the underlying shares on June 16, 2017, provided that the holder continues to serve as a director of the issuer through such date.</footnote>
        <footnote id="F2">Pursuant to the Delphi Management Partners, VIII, L.L.C. (&quot;DMP VIII&quot;) LLC Agreement, the Reporting Person is deemed to hold the options for the benefit of DMP VIII, which is entitled to hold the shares upon issuance. DMP VIII may be deemed the indirect beneficial owner of such shares, and the Reporting Person is a managing member of DMP VIII and may be deemed to share voting and dispositive power over shares held by DMP VIII. The Reporting Person disclaims beneficial ownership of such shares except to the extent of any pecuniary interest therein.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/Matthew T. Potter, Attorney-in-Fact for Deepika Pakianathan</signatureName>
        <signatureDate>2016-06-17</signatureDate>
    </ownerSignature>
</ownershipDocument>
