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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2017-10-02</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001654151</issuerCik>
        <issuerName>Deciphera Pharmaceuticals, Inc.</issuerName>
        <issuerTradingSymbol>DCPH</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001494875</rptOwnerCik>
            <rptOwnerName>Taylor Michael Douglas</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O DECIPHERA PHARMACEUTICALS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>500 TOTTEN POND ROAD</rptOwnerStreet2>
            <rptOwnerCity>WALTHAM</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02451</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>See Remarks</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
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            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.89</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2017-10-02</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
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                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
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                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
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            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2025-12-17</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
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                </underlyingSecurityShares>
            </underlyingSecurity>
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        <derivativeTransaction>
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            </securityTitle>
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                <value>1.89</value>
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            <transactionDate>
                <value>2017-10-02</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
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                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
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            <transactionTimeliness>
                <value></value>
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                <transactionPricePerShare>
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            <expirationDate>
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            </expirationDate>
            <underlyingSecurity>
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                </underlyingSecurityTitle>
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                </underlyingSecurityShares>
            </underlyingSecurity>
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            <ownershipNature>
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        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
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            <transactionDate>
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            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
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                <transactionCode>M</transactionCode>
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            <transactionTimeliness>
                <value></value>
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            <transactionAmounts>
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                <transactionPricePerShare>
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            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <value>2025-12-17</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
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                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>553632</value>
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            </underlyingSecurity>
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            <ownershipNature>
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        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
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            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.89</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2017-10-02</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
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                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
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            <transactionTimeliness>
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                <transactionPricePerShare>
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            <expirationDate>
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            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
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                </underlyingSecurityTitle>
                <underlyingSecurityShares>
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                </underlyingSecurityShares>
            </underlyingSecurity>
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            <ownershipNature>
                <directOrIndirectOwnership>
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                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.95</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2017-10-02</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
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                <equitySwapInvolved>0</equitySwapInvolved>
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            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>38500</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F1"/>
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                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F5"/>
            </exerciseDate>
            <expirationDate>
                <value>2026-09-26</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>217525</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
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                </sharesOwnedFollowingTransaction>
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            <ownershipNature>
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        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
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            </conversionOrExercisePrice>
            <transactionDate>
                <value>2017-10-02</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
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                <equitySwapInvolved>0</equitySwapInvolved>
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            <transactionTimeliness>
                <value></value>
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        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>6.13</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2017-10-02</value>
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                <value></value>
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                <transactionPricePerShare>
                    <footnoteId id="F1"/>
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                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
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            <exerciseDate>
                <footnoteId id="F6"/>
            </exerciseDate>
            <expirationDate>
                <value>2027-06-03</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>247633</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
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        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
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                <value>6.13</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2017-10-02</value>
            </transactionDate>
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                <transactionCode>M</transactionCode>
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                <value></value>
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                <transactionPricePerShare>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
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            <exerciseDate>
                <footnoteId id="F6"/>
            </exerciseDate>
            <expirationDate>
                <value>2027-06-03</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>247633</value>
                </underlyingSecurityShares>
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                    <value>247633</value>
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        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Immediately prior to the closing of the Issuer's initial public offering, these options to purchase common stock of Deciphera Pharmaceuticals, LLC were exchanged for options to purchase common stock of the Issuer on a 1 for 5.65 basis pursuant to that certain Reorganization Agreement and Plan of Merger by and among the Issuer, Deciphera Pharmaceuticals, LLC and the other parties named therein, dated September 26, 2017 (the &quot;Merger Agreement&quot;). These transactions were exempt from Section 16(b) in reliance upon Rule 16b-3 and Rule 16b-6(b).</footnote>
        <footnote id="F2">This stock option award was issued pursuant to Deciphera Pharmaceuticals, LLC's 2015 Equity Incentive Plan.  The option vests in 48 equal monthly installments at the end of each month following the vesting commencement date of September 30, 2015, subject to continued service through such dates.</footnote>
        <footnote id="F3">Represents the total number of options to purchase common stock of the Issuer received upon the exchange of options to purchase common   stock of Deciphera Pharmaceuticals, LLC for options to purchase common stock of the Issuer pursuant to the Merger Agreement.</footnote>
        <footnote id="F4">This stock option award was issued pursuant to Deciphera Pharmaceuticals, LLC's 2015 Equity Incentive Plan.  The option vests in 16 equal quarterly installments at the end of each quarter following the vesting commencement date of March 1, 2014, subject to continued service through such dates.</footnote>
        <footnote id="F5">This stock option award was issued pursuant to Deciphera Pharmaceuticals, LLC's 2015 Equity Incentive Plan.  The option vests in 48 equal monthly installments at the end of each month following the vesting commencement date of July 1, 2016, subject to continued service through such dates.</footnote>
        <footnote id="F6">This stock option award was issued pursuant to Deciphera Pharmaceuticals, LLC's 2015 Equity Incentive Plan.  The option vests in 48 equal monthly installments at the end of each month following the vesting commencement date of May 26, 2017, subject to continued service through such dates.</footnote>
    </footnotes>

    <remarks>President and Chief Executive Officer</remarks>

    <ownerSignature>
        <signatureName>/s/  Thomas P. Kelly, Attorney-in-Fact</signatureName>
        <signatureDate>2017-10-02</signatureDate>
    </ownerSignature>
</ownershipDocument>
