Du Pont was part of General Philip Sheridan's army in the Shenandoah Valley of northern Virginia. He received the Medal of Honor for his handling of a retreat at the Battle of Cedar Creek, allowing Sheridan to win a victory in the battle. During the war, du Pont received two brevets (honorary promotions). The first was to the rank of major, dated September 19, 1864, for gallant service in the battles of Opequon and Fisher's Hill. The second brevet was to the rank of lieutenant colonel, dated October 19, 1864, for distinguished service at the Battle of Cedar Creek, Virginia.