Long served in the Western Theater of the American Civil War. At the outset of the war, on May 24, 1861, Long was promoted to captain in the 1st U.S. Cavalry. On August 3, 1861, he was transferred to the 4th U.S. Cavalry Regiment. On December 31, 1862, Long was wounded in the left shoulder at the Battle of Stones River while commanding Company K of the regiment.