From October 1863 until June 1865, Brannan was chief of artillery of the Department of the Cumberland, where he oversaw the defenses at Chattanooga. He was in the Battle of Missionary Ridge and in the Atlanta Campaign where he participated in the Battle of Resaca, the Battle of Dallas and the Battle of Kennesaw Mountain. He was also at the siege and surrender of Atlanta. He was appointed a brevet major general in both the regular army and in the volunteer forces for Gallant and Meritorious Services in the Atlanta Campaign and in the Field during the Rebellion.