USS Commodore Perry, an armed side wheel ferry, was built in 1859 by Stack and Joyce, Williamsburg, N.Y.; purchased by the Navy 2 October 1861; and commissioned later in the month, Acting Master F. J. Thomas in command.

Commodore Perry sailed from Hampton Roads, Va., 17 January 1862 to join the North Atlantic Blockading Squadron, and on 7 and 8 February took part in the attack, in cooperation with the Army, which resulted in the surrender of Roanoke Island, part of the long campaign through which the Navy secured key coastal points. Commodore Perry took part in the capture of Elizabeth City on 10 February, and the next day captured the schooner Lynnhaven. As operations along the North Carolina coast continued, she joined in the capture of New Bern and Washington in March, and in April took singly or in concert with others of her squadron four schooners and a sloop in the Pasquotank River and Newbegun Creek.

On 3 October 1862, Commodore Perry joined in an Army-Navy expedition against Franklin, Va., and on 10 December, joined an attack against Plymouth, N.C. After another combined expedition against Hertford, N.C., on 30 January 1863, Commodore Perry patrolled constantly in Pamlico and Albemarle Sounds and the streams which enter them, frequently exchanging fire with small detachments of Confederates ashore. Repaired at Norfolk and Baltimore late in 1863, she returned to her squadron in March 1864 for duty in the inland and coastal waters of Virginia on picket, guard, and patrol duty, joining in many amphibious expeditions, until the close of the war. She sailed from Norfolk for New York 12 June 1865, and there was decommissioned 26 June and sold 12 July 1865.