Jackson resigned his position as a court judge to take an appointment as a brigadier general in the Confederate army. In the first year, he served at the battle of Cheat Mountain in western Virginia before he resigned to take an assignment to command a division of Georgia State Troops in defense of Savannah. In December 1861, he was promoted to major general, and aide to General W.H.T. Walker. However, in September 1861, he was re-commissioned as a brigadier. He organized troops during the Atlanta campaign before he marched to Tennessee. He was captured at the Battle of Nashville in December 1864.