Pettus served in the Western Theater of the American Civil War. During the Stones River Campaign, he was captured by Union soldiers on December 29, 1862, and exchanged a short time later for Union soldiers. Pettus was captured again on May 1, 1863, while part of the surrendered garrison that had been defending Port Gibson in Mississippi. He managed to escape and return to his own lines. Pettus was promoted to colonel on May 28, and given command of the 20th Alabama.