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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2020-10-29</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001593899</issuerCik>
        <issuerName>Atea Pharmaceuticals, Inc.</issuerName>
        <issuerTradingSymbol>AVIR</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001657434</rptOwnerCik>
            <rptOwnerName>Hack Andrew A. F.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O BAIN CAPITAL LIFE SCIENCES</rptOwnerStreet1>
            <rptOwnerStreet2>INVESTORS, 200 CLARENDON STREET</rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02116</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series D Convertible 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>3383190</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 D-1 Convertible 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>1982469</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">All series of convertible preferred stock will automatically convert into shares of the Issuer's common stock on a 1-for-1 basis immediately prior to the closing of the Issuer's initial public offering and have no expiration date.</footnote>
        <footnote id="F2">Represents shares held directly by Bain Capital Life Sciences Fund II, L.P. (&quot;BCLS II&quot;) and BCIP Life Sciences Associates, LP (&quot;BCIPLS&quot;) and, together with BCLS II, the &quot;Bain Capital Life Sciences Entities&quot;).</footnote>
        <footnote id="F3">Bain Capital Life Sciences Investors, LLC (&quot;BCLSI&quot;) (i) is the ultimate general partner of BCLS II, and (ii) governs the investment strategy and decision-making process with respect to investments held by BCIPLS. Dr. Hack is a Managing Director of BCLSI. By virtue of the relationships described in this footnote, Dr. Hack may be deemed to share voting and dispositive power with respect to the securities held by the Bain Capital Life Sciences Entities. Dr. Hack disclaims beneficial ownership of such securities except to the extent of his pecuniary interest therein.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Andrew A.F. Hack</signatureName>
        <signatureDate>2020-10-29</signatureDate>
    </ownerSignature>
</ownershipDocument>
