When the Civil War began, Battle received a commission as major of the 3rd Alabama Infantry on April 28, 1861, and was sent with the regiment to Norfolk, Virginia. On July 31, he was promoted to lieutenant colonel of the regiment. He fought at the Battle of Seven Pines and was promoted to colonel on May 31, 1862. He missed the Seven Days Battles, but returned to the army in time for the Maryland Campaign, in September 1862, fighting at the battles of South Mountain and Antietam. He was injured after falling from his horse just before the Chancellorsville Campaign and was forced to relinquish command. Although he re-assumed command just a day later, his injuries were aggravated when his horse jumped a ditch, forcing him to turn over command again.