In 1861, Granger was on duty in Texas when he was captured and then paroled by the Confederate army. In September 1861 he was promoted to major. He served in a desk job until October 1862 when he received his commission as a brigadier general. Throughout the war, he was relegated to camp and garrison duty in Kentucky, Tennessee, and northern Alabama. He commanded the Union forces during the action at Decatur. At the end of the war, he was brevetted as a major general.