On May 2, 1862, Root was commissioned colonel of the 94th New York Volunteer Infantry Regiment. Root fought with his regiment at the Battle of Cedar Mountain on August 9, 1862, and fought and was wounded at the Second Battle of Bull Run on August 30, 1862. On November 15, 1862, he returned to duty to command the 1st Brigade, 2nd Division, I Corps of the Army of the Potomac until May 11, 1863, when he resumed command of his regiment. As brigade commander, he commanded the brigade at the Battle of Fredericksburg and the Battle of Chancellorsville.