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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2016-06-02</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001485003</issuerCik>
        <issuerName>Eleven Biotherapeutics, Inc.</issuerName>
        <issuerTradingSymbol>EBIO</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001465837</rptOwnerCik>
            <rptOwnerName>Boxer Capital, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>11682 EL CAMINO REAL, SUITE 320</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SAN DIEGO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92130</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001465836</rptOwnerCik>
            <rptOwnerName>Boxer Asset Management Inc.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>CAY HOUSE, EP TAYLOR DRIVE N7776</rptOwnerStreet1>
            <rptOwnerStreet2>LYFORD CAY</rptOwnerStreet2>
            <rptOwnerCity>NEW PROVIDENCE</rptOwnerCity>
            <rptOwnerState>C5</rptOwnerState>
            <rptOwnerZipCode></rptOwnerZipCode>
            <rptOwnerStateDescription>BAHAMAS</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001015747</rptOwnerCik>
            <rptOwnerName>LEWIS JOSEPH</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>CAY HOUSE, EP TAYLOR DRIVE N7776</rptOwnerStreet1>
            <rptOwnerStreet2>LYFORD CAY</rptOwnerStreet2>
            <rptOwnerCity>NEW PROVIDENCE</rptOwnerCity>
            <rptOwnerState>C5</rptOwnerState>
            <rptOwnerZipCode></rptOwnerZipCode>
            <rptOwnerStateDescription>BAHAMAS</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001468223</rptOwnerCik>
            <rptOwnerName>MVA Investors, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>11682 EL CAMINO REAL, SUITE 320</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SAN DIEGO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92130</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>2255572</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F1"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>475000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">These securities are owned directly by Boxer Capital, LLC (&quot;Boxer Capital&quot;), which may be deemed to be a member of a &quot;group&quot; for purposes of Section 13(d) of the Securities Exchange Act of 1934, as amended, consisting of (i) Boxer Capital, (ii) Boxer Asset Management Inc. (&quot;Boxer Management&quot;), (iii) MVA Investors, LLC (&quot;MVA Investors&quot;) and (iv) Joseph C. Lewis (collectively, the &quot;Boxer Group&quot;), and indirectly by Boxer Management and Mr. Lewis, by virtue of their ownership in Boxer Capital.</footnote>
        <footnote id="F2">These securities are owned directly and solely by MVA Investors, which has sole voting and dispositive power with respect to these securities.  Each member of the Boxer Group other than MVA Investors disclaims beneficial ownership of these securities to the extent it or he does not have a pecuniary interest therein.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Boxer Capital, LLC, By: /s/ Aaron I. Davis, Aaron I. Davis</signatureName>
        <signatureDate>2016-06-06</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Boxer Asset Management, Inc., By: /s/ Jefferson R. Voss, Jefferson R. Voss</signatureName>
        <signatureDate>2016-06-06</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>MVA Investors, LLC, By: /s/ Aaron I. Davis, Aaron I. Davis</signatureName>
        <signatureDate>2016-06-06</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Joseph C. Lewis, Joseph C. Lewis</signatureName>
        <signatureDate>2016-06-06</signatureDate>
    </ownerSignature>
</ownershipDocument>
