Prior to delivery to the Boston Prize Court on 7 July, she was used in the search for the Confederate raider CSS Tacony.

After condemnation, Cherokee was purchased by the Government, outfitted at Boston Navy Yard, and commissioned 21 April 1864, Acting Volunteer Lieutenant J. F. Nickels in command.

In addition to contributing to Union victory by cutting the Confederacy off from overseas sources of supply, this squadron repeatedly bombarded coastal defenses, and cooperated with the Army in amphibious expeditions up the many bays, inlets, and rivers of the serrated coast.

On 30 January she was ordered close inshore at New Inlet to reconnoiter the Half Moon Battery, where she discovered a large party of Confederates approaching the fortifications recently secured by Union troops.

Cherokee threw heavy fire ashore, which drove the Confederates away after three determined rushes at the Union lines.