With the outbreak of the Civil War and Virginia's subsequent secession, Patton enlisted in the Confederate Army in the spring of 1861 and was elected to serve as a major in the 7th Virginia Infantry. He was promoted to lieutenant colonel on April 27, 1862. Patton took command of the regiment in June 1862 following the promotion of the previous colonel, James L. Kemper, to the command of the brigade. He was badly wounded at Second Manassas on August 30, 1862, and spent the remainder of the year back home in Fredericksburg recuperating. Patton was elected to the Virginia Senate in 1863, but chose instead to return to his regiment.