Enlisting in the Confederate army in 1861, he served as a judge in Confederate courts. Promoted in June to brigadier general, he later led troops during the Western Virginia campaign, seeing action at the Battle of Cheat Mountain. In December, he was promoted to major general of state militia for Georgia. Returning to Confederate service in September 1863, he led a brigade during the later part of the Atlanta Campaign. He commanded a brigade in William B. Bate's division in John Bell Hood's Franklin-Nashville Campaign. Jackson was captured at the Battle of Nashville and was paroled from Fort Warren, Massachusetts, on July 8, 1865.