The third USS Philadelphia was the flagship of Rear Admiral Samuel Phillips Lee when he commanded the North Atlantic Blockading Squadron during the American Civil War.

She was operating as a trading vessel between Aquia Creek, Virginia and Washington, D.C. at the outbreak of the Civil War.

Philadelphia — Lieutenant William Nicholson Jeffers commanding — operated on the Potomac River as a patrol vessel.

She continued to operate on the Potomac River until October 1861, primarily transporting troops downriver to Fort Washington.

Philadelphia took part in the expedition to Hatteras Inlet in January and served as flag-steamer to Flag Officer Louis M. Goldsborough at the battle of Roanoke Island North Carolina on 7–8 February.