Between 1861 and 1865, "Fulton" was chartered by the U. S. Department of War in the Army Transport Service, for use as an army transport, at a cost of 1,200 dollars per day. She made trips from New York to ports on the Southern coast. Captain J. A. Wotton and thousands of military men traveled with her on these excursions. She worked in operations with the South Atlantic Blockading Squadron throughout the war.