Assigned to what became the IX Corps in the Army of the Potomac, Scammon then commanded the 1st Brigade, Kanawha Division. During the Maryland Campaign, he led his men in an attack up the slopes of South Mountain. When Brig. Gen. Jacob D. Cox briefly assumed command of the IX Corps, Scammon temporarily commanded the Kanawha Division, while Col. Hugh Ewing commanded Scammon's brigade. He fought well at the Battle of Antietam, where his men were counterattacked by late-arriving Confederate reinforcements under A.P. Hill.