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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2018-07-31</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001488613</issuerCik>
        <issuerName>Foundation Medicine, Inc.</issuerName>
        <issuerTradingSymbol>FMI</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001585001</rptOwnerCik>
            <rptOwnerName>Yeshwant Krishna</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O FOUNDATION MEDICINE, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>150 SECOND STREET</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02141</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2018-07-31</value>
                <footnoteId id="F1"/>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>U</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>5786</value>
                    <footnoteId id="F2"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>137.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Foundation Medicine, Inc., a Delaware corporation (the &quot;Company&quot;) entered into an Agreement and Plan of Merger, dated as of June 18, 2018, as amended (the &quot;Merger Agreement&quot;), with Roche Holdings, Inc., a Delaware corporation (&quot;Parent&quot; or &quot;Roche&quot;), and 062018 Merger Subsidiary, Inc., a Delaware corporation and a wholly owned subsidiary of Parent (&quot;Merger Sub&quot;). Pursuant to the Merger Agreement, Parent caused Merger Sub to conduct a tender offer (the &quot;Tender Offer&quot;) for all of the issued and outstanding shares of common stock, par value $0.0001 per share, of the Company, at a price of $137 per share. On July 31, 2018, Merger Sub irrevocably accepted for payment all shares that were validly tendered and not withdrawn. On July 31, 2018, following consummation of the Tender Offer, Merger Sub merged with and into the Company.</footnote>
        <footnote id="F2">The amount reported represents the number of shares sold by the reporting person in connection with the Tender Offer by Roche.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Robert W. Hesslein, Attorney-in-Fact for Krishna Yeshwant</signatureName>
        <signatureDate>2018-08-02</signatureDate>
    </ownerSignature>
</ownershipDocument>
