In 1861, Brannon was appointed brigadier general. He served on the South Atlantic coast before he was transferred to the Army of the Cumberland. He was involved in the Tullahoma campaign and at the Battle of Chickamauga. In October 1863, he was relieved of his command during the reorganization of the army, and he was given the position of chief of artillery of the Army of the Cumberland. In this capacity, he was involved in the defense of Chattanooga, and the Atlanta campaign. At the end of the war, he was brevetted major general.