When the Civil War began, Lewis joined the Confederate army as the third lieutenant of Company A, 1st North Carolina Regiment ("Bethel"). His first fighting came in the Battle of Big Bethel on June 10, 1861. By January 1862, he had been promoted to major and took part in the Battle of New Bern. For his actions at New Bern, he was promoted to lieutenant colonel of the 33rd North Carolina Infantry. Lewis fought with the regiment at the Seven Days Battle and the Battle of Malvern Hill. During the later months of 1862, he took part in the defense of Richmond.