In May 1861, Howard was elected colonel of the 3rd Maine Infantry. He commanded a brigade at the Battle of First Manassas, and although his brigade was unsuccessful, he received a commission as a brigadier general. During the Peninsula campaign, he led a brigade of the II corps. He lost his right arm at the Battle of Seven Pines. He quickly recovered in time for service in the Battle of First Manassas. During the Battle of Antietam, he took command of a division, which he would lead into the subsequent Battle of Fredericksburg. In March 1863, he was promoted to major general, and assigned to command of the XI corps. In May, at the Battle of Chancellorsville, his forces were routed by a Confederate flank attack. At the Battle of Gettysburg in July, he performed well, but not enough to improve his reputation. The XI Corps was sent west to Chattanooga, and then Howard was transferred to command of the IV Corps during the Atlanta campaign. In the campaign of the Carolina, he was assigned command of the Army of Tennessee after the death of General James B. McPherson. Howard continued to serve in the army after the end of the war.