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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2021-12-15</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001852595</rptOwnerCik>
            <rptOwnerName>Pitman Jama</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O DECIPHERA PHARMACEUTICALS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>200 SMITH STREET</rptOwnerStreet2>
            <rptOwnerCity>WALTHAM</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02451</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>See Remarks</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2021-12-15</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>8300</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>25438</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>9.23</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2021-12-15</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>62971</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <value>2031-12-14</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>62971</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>62971</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The reporting person was awarded 8,300 Restricted Stock Units (&quot;RSUs&quot;) under the Issuer's 2017 Stock Option and Incentive Plan (the &quot;2017 Plan&quot;). Each RSU represents a contingent right to receive one share of the Issuer's Common Stock. The RSUs shall vest in two equal installments on June 15, 2022 and June 15, 2023, subject to continued service with the Issuer or a Subsidiary (as defined in the 2017 Plan) through such dates. The RSUs may be settled only by delivering shares of the Issuer's Common Stock, and thus, the grant is being reported in Table 1 as allowed per SEC guidance.</footnote>
        <footnote id="F2">This number includes (i) 5,280 RSUs issued pursuant to the 2017 Plan which vest in three (3) equal annual installments on each of February 15, 2022, 2023 and 2024; and (ii) 8,300 RSUs issued pursuant to the 2017 Plan which vest in equal annual installments over four (4) years beginning on February 15, 2022. Each RSU represents a contingent right to receive one (1) share of the Issuer's Common Stock. The RSUs may be settled only by delivering shares of the Issuer's Common Stock, and thus, the grant is being reported in Table 1 as allowed per SEC guidance.</footnote>
        <footnote id="F3">Includes 145 shares acquired under the Issuer's 2017 Employee Stock Purchase Plan on November 12, 2021.</footnote>
        <footnote id="F4">This stock option was issued pursuant to the 2017 Plan.  The option shall vest in two equal installments on June 15, 2022 and June 15, 2023, subject to continuous service with the Issuer or a Subsidiary (as defined in the 2017 Plan) through each vesting date.</footnote>
    </footnotes>

    <remarks>Title:  SVP, Regulatory, Quality, &amp; Portfolio Management</remarks>

    <ownerSignature>
        <signatureName>/s/ Jeffrey Held, Attorney-in-Fact</signatureName>
        <signatureDate>2021-12-17</signatureDate>
    </ownerSignature>
</ownershipDocument>
