When the Civil War started in 1861 Corput joined the Confederate States Army. He was commissioned as a Third Lieutenant (1861) in the "Cherokee Artillery" battery; a unit recruited from the Floyd and Cherokee counties. Several of his relatives joined the unit, too, his brother Felix being the Quartermaster Sergeant. The unit was surrendered during the Siege of Vicksburg, but quickly returned to the field afterwards. By 1864 Corput had been promoted to captain and commanded the battery. At the Battle of Resaca its four 12-pounder Napoleons were captured. Corput himself became a prisoner of war on April 12, 1865 at Salisbury, North Carolina. He was held prisoner at Camp Chase, Ohio until paroled in October.