Sailing from New York City on 20 June to New London, Connecticut, for fitting out and thence proceeding to Newport, Rhode Island, to load torpedoes, N-5 began patrols off New England and in Long Island Sound on watch against attacks on coastal shipping by German U-boats.
In August and September she deployed under tow by a decoy ship, the sailing vessel USS Charles Whittemore.
[1] On 7 September, after parting tow from her escort in a heavy sea, she was mistaken by an armed transport for a U-boat and was fired upon.
She continued her patrols until 24 October when she put into New York Navy Yard for repairs, and remained there following the Armistice with Germany until sailing to Philadelphia, Pennsylvania, on 21 February 1919.
On 1 October, N-5 sailed to Philadelphia Navy Yard for extensive overhaul lasting until 7 April 1921 when she returned to New London, once again being placed in ordinary.