In October 1861, Thomas became colonel of the 35th Georgia Infantry. The regiment was attached to Brig. Gen Joseph R. Anderson's brigade, which was initially stationed in Georgia, but during the Peninsula Campaign was sent to the Richmond area to reinforce Joe Johnston's army. On May 27, 1862, the brigade was added to the newly created division of Maj. Gen A.P. Hill, soon to be known as the "Light Division". While commanding the regiment, Thomas suffered a minor wound at the Battle of Beaver Dam Creek (Mechanicsville) during the Seven Days Battles. Anderson was wounded at Glendale and afterwards resigned his commission to manage the Tredegar Iron Works in Richmond. Thomas then became permanent commander of the brigade and on November 1, he was promoted to brigadier general, participating in all of the major battles and campaigns fought by the Army of Northern Virginia.