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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2017-09-27</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001547100</rptOwnerCik>
            <rptOwnerName>Ratcliffe Liam</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>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series B-1 Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>839110</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series B-2 Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1118722</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series B-1 Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>279703</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series B-2 Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1118722</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series C Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>372883</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                    <footnoteId id="F4"/>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>17.00</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F6"/>
            </exerciseDate>
            <expirationDate>
                <value>2027-09-26</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>67800</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Represents preferred stock of Deciphera Pharmaceuticals, LLC (&quot;Deciphera, LLC&quot;).  Upon the closing of the Issuer's initial public offering, each share of preferred stock will automatically be converted into 5.65 shares of common stock of the Issuer.</footnote>
        <footnote id="F2">The preferred stock is currently owned by NLV-3 Deciphera, Inc., a wholly-owned subsidiary of New Leaf Ventures III, L.P. (&quot;NLV III&quot;) whose sole purpose is to hold equity interests in Deciphera, LLC.  Pursuant to that certain Reorganization Agreement and Plan of Merger by and among the Issuer, Deciphera, LLC and the other parties named therein, dated September 26, 2017 and in the form attached as Exhibit 2.1 to the Issuer's registration statement on Form S-1, File No. 333-220299 (the &quot;Merger Agreement&quot;), the Issuer will issue shares of its common stock to  NLV III in exchange for the shares of Deciphera, LLC. New Leaf Venture Associates III, L.P. (&quot;NLV Associates III&quot;) is the sole general partner of NLV III. New Leaf Venture Management III, L.L.C. (&quot;NLV Management III&quot;) is the sole general partner of NLV Associates III. New Leaf Venture Partners, L.L.C.</footnote>
        <footnote id="F3">(Continued from Footnote 2) (&quot;NLVP&quot;) is the investment adviser of NLV III. Each of NLV Associates III and NLV Management III disclaim beneficial ownership of these securities and this report shall not be deemed an admission that NLV Associates III or NLV Management III are beneficial owners of such securities for purposes of Section 16 or for any other purpose, except to the extent of their respective pecuniary interests therein. Each of the Reporting Person, Jeani Delagardelle, Ronald M. Hunt and Vijay K. Lathi (each, a &quot;Member&quot; and collectively, the &quot;Members&quot;) is a member of NLV Management III and may be deemed to have shared voting and dispositive power of these securities. Each of the Members disclaims beneficial ownership of these securities and this report shall not be deemed an admission that any of them is the beneficial owner of such securities for purposes of Section 16 or for any other purpose, except to the extent of their respective pecuniary interests therein.</footnote>
        <footnote id="F4">The preferred stock is currently owned by NLV-G Deciphera, Inc., a wholly-owned subsidiary of New Leaf Biopharma Opportunities I, L.P. (&quot;Biopharma I&quot;) whose sole purpose is to hold equity interests in Deciphera, LLC.  Pursuant to the Merger Agreement, the Issuer will issue shares of its common stock to Biopharma I in exchange for shares of Deciphera, LLC. New Leaf BPO Associates I, L.P. (&quot;NLBA I&quot;) is the sole general partner of Biopharma I. NLV Management III is the sole general partner of NLBA I. NLVP is the investment adviser of Biopharma I.</footnote>
        <footnote id="F5">(Continued from Footnote 4) Each of NLBA I and NLV Management III disclaim beneficial ownership of these securities and this report shall not be deemed an admission that NLBA I or NLV Management III are beneficial owners of such securities for purposes of Section 16 or for any other purpose, except to the extent of their respective pecuniary interests therein. Each of the Members may be deemed to have shared voting and dispositive power of these securities. Each of the Members disclaims beneficial ownership of these securities and this report shall not be deemed an admission that any of them is the beneficial owner of such securities for purposes of Section 16 or for any other purpose, except to the extent of their respective pecuniary interests therein.</footnote>
        <footnote id="F6">This stock option award was issued pursuant to Deciphera Pharmaceuticals, Inc.'s 2017 Stock Option and Incentive Plan.  This option vests in 48 equal monthly installments at the end of each month following the vesting commencement date of September 14, 2015, subject to continued service through such dates.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Thomas P. Kelly, Attorney-in-Fact</signatureName>
        <signatureDate>2017-09-28</signatureDate>
    </ownerSignature>
</ownershipDocument>
