In 1862 Thomas was sent to serve in the Western Theater, and was given command of the artillery belonging to a brigade in the Army of Mississippi as of March 18. Eight days later Thomas was appointed assistant inspector general of the brigade, a post he held until that summer. Assigned to the staff of Maj. Gen. Jones M. Withers, Thomas fought at the Battle of Shiloh on April 6–7, performing a "commendable part in the battle..." In July he was assigned command of the army's Reserve Corps artillery, a position Thomas would hold for the rest of the year. He also participated in the Kentucky Campaign that autumn, and then took a brief sick leave. Thomas returned to duty in time to fight during the Battle of Stone's River in late 1862.