Neil participated in the Western Theater of the American Civil War, being wounded during the Battle of Shiloh and seeing action during the Vicksburg and Chattanooga campaigns. For bravery upon the field, he was promoted to captain on April 14, 1864. During the Atlanta Campaign, he fought in the battles of Resaca, Dallas, Ezra Church, and Lovejoy's Station before his promotion to major on January 23, 1865. At the end of the war, he mustered out at the rank of lieutenant colonel.