The Valley Guards were incorporated into the 10th Virginia Infantry after the war began. Warren was commissioned lieutenant colonel of the 10th Virginia on August 1, 1861. As the lieutenant colonel, Warren served at the First Battle of Bull Run, where the regiment served in the brigade of Brig. Gen. Edmund Kirby Smith. He became colonel on May 8, 1862, after Colonel Simeon B. Gibbons was killed at the Battle of McDowell in May 1862.