For the remainder of the war, she carried mail, supplies, officers, and seamen from Northern ports to and from the ships and stations of her squadron.

She departed Newport News, Virginia, before dawn 11 December hunting a "steamer burning soft coal" reportedly attempting to run the blockade near the entrance to Chesapeake Bay.

Shortly thereafter the blockade runner, carrying arms, lead, bacon, and uniforms for Robert E. Lee's army, exploded.

She scored again 16 December 1864 when, with USS Mount Vernon, she captured and burned schooner G. O. Bigelow in ballast at Bear Inlet, North Carolina.

After the war, New Berne continued service as a supply ship, but for two periods in ordinary, 5 December 1866 to 8 February 1867 and 5 April to 26 November 1867, until decommissioning 29 March 1868.