During the Civil War, Raynolds participated in the Battle of Cross Keys during the Valley Campaign of 1862 and a year later was in charge of fortifications in the defense of the military arsenal at Harpers Ferry, West Virginia. On March 13, 1865, Raynolds was brevetted brigadier general for meritorious service during the Civil War. Raynolds retired from the army on March 17, 1884, with the permanent rank of colonel.