Kilty returned to the Active List on January 6, 1859, and was stationed in Baltimore in 1860 as a recruiting officer. From 1861 Kilty commanded the ironclad gunboat of the Mississippi Flotilla, and saw action at Island No. 10 and Fort Pillow. He commanded an expedition to White River, Arkansas, and during the operation, on June 17, 1862, was severely wounded, causing the loss of his left arm. Kilty received his commission as a captain on July 16, 1862, and spent the years 1863–64 on ordnance duty. He commanded the ironclad frigate in the North Atlantic Squadron from 1864 to 1865, and was promoted to commodore on July 25, 1866, and served as the Commandant of the Norfolk Navy Yard.