[2] Emma was captured on 24 July 1863 by the Army transport SS Arago off the coast of Wilmington, North Carolina on its third voyage.

[3][4] Emma arrived at Newport News, Virginia, 7 November 1863 to patrol with the North Atlantic Blockading Squadron until the end of the war.

Enforcing the blockade, she played a significant role in the Navy's indispensable contribution to victory through isolating the South from oversea sources of supply.

[4] On 26 April 1865, Emma sailed from Fort Caswell, North Carolina, with an urgent message from General William Tecumseh Sherman to Rear Admiral John A. Dahlgren, commanding the South Atlantic Blockading Squadron, which warned the Admiral that Confederate President Jefferson Davis and his cabinet, not yet located, might attempt to escape by way of Florida to Cuba.

Emma put into Key West, Florida, on this cruise, then returned to patrol the Carolina coast until 24 August, when she arrived at Boston, Massachusetts.