Corse joined the 6th Iowa Infantry as its Major in July 1861 and initially served under Maj. Gen. John C. Fremont. He then served on the staff of Maj. Gen. John Pope early the following year during the Battle of Island Number Ten and associated engagements. He returned to field duty with his regiment and fought in the Siege of Corinth, being promoted to lieutenant colonel. He was promoted to brigadier general of volunteers on August 11, 1863, in recognition of his service at the Siege of Vicksburg. Assigned command of the 4th Brigade, 4th Division, XV Corps, in the Federal Army of the Tennessee, Corse participated in the Chattanooga Campaign. After recuperating from an injury suffered at Missionary Ridge, Corse returned to active duty as the inspector general on Maj. Gen. William Tecumseh Sherman's staff. In July 1864, he returned to field duty in command of a division in XVI Corps.