Following the secession of Tennessee and the beginning of the American Civil War, Maney joined the Rock City Guards, a Nashville militia. He subsequently enlisted in the Confederate States Army as a Captain in the 11th Tennessee Volunteer Infantry. On May 6, 1861, he was promoted to colonel of the 1st Tennessee. He served in western Virginia, first under Robert E. Lee at the Battle of Cheat Mountain and later under Thomas J. "Stonewall" Jackson at Bath and Romney.