In 1861 Sullivan organized the Sixth Indiana Volunteers. He later became a colonel in the 13th Indiana. He served at Rich Mountain in western Virginia before rising to command a brigade at Kernstown during the Shenandoah Valley campaign of 1862. He was commissioned a brigadier general and was sent to the West. In the autumn of 1862, he commanded the District of Jackson of the Army of Tennessee. He fought at Iuka and Corinth before he relinquished his command. He transferred back to the East to serve as a division commander in the Department of West Virginia. He served at New Market and in the Lynchburg expedition. In 1864 he was replaced and removed further away from the fighting in West Virginia and never again oversaw a significant command. He resigned in May 1865.