She was named after Commodore Oliver Hazard Perry (1785–1819), a naval officer who had commanded American forces on Lake Erie in the War of 1812.

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

[1] On 9 July 1862, at 2 a. m., the U.S. gunboats Commodore Perry, Shawsheen and Ceres, left Plymouth, N.C., and steamed up the Roanoke River on an expedition to Hamilton, where a large force of Confederates was reported to be stationed.

At Hamilton we landed 100 men, soldiers and sailors, and one field piece, but the rebels, who fired on us from high banks, where they were comparatively safe, were afraid to meet us.

Acting Master Mac Diarmid, in command of the Ceres, in his report of the affair to his superior officer, under the date of 10 July 1862, says : "When within a few miles of Hamilton, was fired on by the enemy from the left bank with small arms.

As operations along the North Carolina coast continued, she joined in the capture of New Berne 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 New Begun Creek.

[2][3] After another combined expedition against Hertford, North Carolina 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.