In 1861, Stewart accepted a commission as a major in the artillery for the Tennessee Militia. He received the rank of brigadier general in November 1861 in the Confederate Army. Known as "Old Straight," Stewart served in the Army of Tennessee during the battle of Chickamauga, the Atlanta Campaign, the Franklin-Nashville Campaign, and the Carolinas campaign. In 1863, he was promoted to major general. In 1864, Stewart was promoted to lieutenant general. He was paroled with General Joseph Johnston's army in 1865.
