When the American Civil War began in 1861, Archer was stationed in Fort Walla Walla in the Washington Territory. He resigned his commission on May 14, traveled to the South, and joined the Confederate Army as a captain in the Provisional Army. He soon was named colonel of the 5th Texas Infantry Regiment, serving in the brigade organized by former Texas Senator Louis T. Wigfall. After Brig. Gen. John Bell Hood assumed command, the Texas Brigade fought in the Peninsula Campaign in Virginia. Archer led his regiment at Eltham's Landing. At Seven Pines, the Texas Brigade was held in reserve and Archer did not see any action. He was not especially popular with the soldiers in the 5th Texas, who considered him a martinet.