Assigned to the South Atlantic Blockading Squadron, Chenango left New York City for Hampton Roads, Virginia on 15 April 1864.

Before she reached the open sea, her port boiler exploded, scalding 33 men, 28 fatally, with another suffering a head concussion from collateral damage.

A raging fire was brought under control and extinguished by the courageous work of her crew, and the ship was towed back to New York for repairs.

She operated in the Charleston area as well as along the Georgia coast, and on 25 February captured the blockade runner Elvira, laden with cotton and tobacco.

Chenango cleared Charleston on 16 May 1865, towing the armed steamer USS Cambridge to Philadelphia, Pennsylvania, where she arrived on 20 May, was decommissioned on 1 July 1865, and sold 28 October 1868.