Ducat began his war service on May 2, 1861, as 2nd lieutenant of the 12th Illinois Infantry Regiment. He became 1st lieutenant on May 11, 1861, captain on August 1, 1861, major on September 24, 1861, and lieutenant colonel on April 1, 1862. He was wounded at the Battle of Fort Donelson in February 1862. After his service with 12th Illinois Infantry ended on October 30, 1862, Ducat served as the Inspector General of two major Federal armies in the Western Theater of the American Civil War, mainly in the Army of the Cumberland. He was discharged on February 19, 1864.