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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2014-06-23</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001439222</issuerCik>
        <issuerName>AGIOS PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>AGIO</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001508052</rptOwnerCik>
            <rptOwnerName>Flagship Ventures Fund 2007, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE MEMORIAL DRIVE, 7TH FLOOR</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001222012</rptOwnerCik>
            <rptOwnerName>AFEYAN NOUBAR</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE MEMORIAL DRIVE, 7TH FLOOR</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001255927</rptOwnerCik>
            <rptOwnerName>KANIA EDWIN M JR</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE MEMORIAL DRIVE, 7TH FLOOR</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001508053</rptOwnerCik>
            <rptOwnerName>Flagship Ventures 2007 General Partner LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE MEMORIAL DRIVE, 7TH FLOOR</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2014-06-23</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>J</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>1930369</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1930369</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Effective June 23, 2014, Flagship Ventures Fund 2007, L.P. (&quot;Flagship 2007&quot;), the direct holder of the shares reported herein, distributed in-kind, and without consideration, a total of 1,930,369 shares of the Issuer's common stock to Flagship 2007's general and limited partners.</footnote>
        <footnote id="F2">These shares are held by Flagship 2007.  Flagship Ventures 2007 General Partner, LLC (&quot;Flagship 2007 LLC&quot;) is the sole general partner of Flagship 2007.  Noubar B. Afeyan, Ph.D. and Edwin M. Kania, Jr. are the managers of Flagship 2007 LLC and, as such, may be deemed to share voting and investment power with respect to all shares held by Flagship 2007.  Each of the filing persons disclaims beneficial ownership of these shares except to the extent of his or its pecuniary interest therein.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>FLAGSHIP VENTURES FUND 2007, L.P., By: Flagship Ventures 2007 General Partner, LLC, its general partner, By: /s/ Noubar B. Afeyan, Ph. D., Name: Noubar B. Afeyan, Ph. D., Title: Manager</signatureName>
        <signatureDate>2014-06-25</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>FLAGSHIP VENTURES 2007 GENERAL PARTNER LLC, By: /s/ Noubar B. Afeyan, Ph. D, Name: Noubar B. Afeyan, Ph. D., Title: Manager</signatureName>
        <signatureDate>2014-06-25</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Noubar B. Afeyan, Ph. D.</signatureName>
        <signatureDate>2014-06-25</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Edwin M. Kania, Jr.</signatureName>
        <signatureDate>2014-06-25</signatureDate>
    </ownerSignature>
</ownershipDocument>
