During the American Civil War, Countess was employed by the Confederacy as an unarmed transport, likely under contract. The steamer was retained by Major General John G. Walker for the evacuation of Alexandria, Louisiana in March 1864 during the Red River campaign. She loaded slaves, tools, and property from the city on March 13 and escaped upriver with the other Confederate steamers, reaching Grand Ecore by March 17. She was incorrectly reported to have been burned by Confederate forces after grounding in the Alexandria rapids during the evacuation of the city, and continued to operate late into the war. This report arose from the misidentification of the burned Alexandria-Pineville ferry as Countess on March 15 by Union Lieutenant Commander Seth Ledyard Phelps in his post-battle report. She was employed as a flag of truce vessel in January 1865 and transported troops across the Red River at Shreveport in April of that year. After the Confederate surrender, Countess continued to operate as a packet carrying cotton on the Red River.
