Perkins spent the first months of the Civil War in Sumpter, operating on anti-slavery patrols. Under Admiral Farragut, he participated in the passing of Forts Jackson and St. Philip, the capture of Governor Moore and three ships of the Montgomery Flotilla, and the surrender of New Orleans in April 1862. He also fought at Port Hudson and Whitehall’s River in July 1862, at the capture of Mary Sorley and Tennessee, the Battle of Mobile Bay, and at Forts Powell, Gaines, and Morgan in August 1864.
Following the Civil War, Lieutenant Commander Perkins served as Superintendent of Ironclads at New Orleans, executive officer of the steam sloop Lackawanna in the North Pacific, and had ordnance duty at the Boston Navy Yard. Promoted to the rank of Commander in early 1871, he spent the next decade as Commanding Officer of the storeship Relief and gunboat Ashuelot and had further shore duty at Boston.
Perkins was promoted to captain in 1882 and commanded the Pacific Station flagship USS Hartford during the mid-1880s. In 1991, he was transferred to the Retired List but in 1896 received a Congressionally authorized promotion to the retired rank of commodore in recognition of his gallantry and skill during the Battle of Mobile Bay three decades earlier.
Commodore Perkins died at Boston on 28 October 1899. A large statue of him was erected on the grounds of the New Hampshire State Capitol at Concord.