Branch entered the Confederate Army, in May 1861, as a private in the Raleigh Rifles. Later that month he accepted the office of state quartermaster general, but resigned it for service in the field. In September he was elected colonel of the 33rd North Carolina. He was appointed brigadier general in January 1862. After the Battle of New Bern, his brigade was attached to A.P. Hill's Division of Stonewall Jackson's Corps. He was the senior brigadier general in Hill's division. Branch's brigade fought at the Battle of Hanover Courthouse, the Seven Days Battles, Cedar Mountain, Second Manassas, Chantilly, and Harper's Ferry