The fort was evacuated in April 1861 under orders from General David E. Twiggs at the start of the Civil War. During John R. Baylor's invasion of New Mexico, only 20 Confederate States Army troops manned the fort. On the night of 4 August 1861, Mescalero Apaches raided a nearby cattle pen, and during the pursuit on 11 August, Lt. Reuben E. Mays and all but one of his 13-man patrol were killed in an ambush. This defeat convinced Baylor to staff the fort with three officers and 70 enlisted men. The Confederates evacuated the fort and all other posts west of Fort Clark in August 1862.