Scofield enlisted as a private in the Union Army in April 1861 and was assigned to Company H of the 2nd Iowa Infantry. He was promoted to second and then to first lieutenant, taking command of the company in February 1862 at the time of the Battle of Fort Donelson. He was adjudant to Brig. Gen. Jacob G. Lauman at the Battle of Shiloh where Scofield was wounded in the leg. He returned to duty within a month. He was transferred to the staff of Brig. Gen. John McArthur at the Battle of Vicksburg and the Battle of Memphis.