At the start of the war, Carr was instrumental in the recruitment of the 2nd New York Volunteer Infantry Regiment and was appointed its colonel on May 14, 1861. Assigned to Fort Monroe, Virginia, the regiment took part in the engagement at Big Bethel. Carr served in the Army of the Potomac throughout the Peninsula Campaign and Seven Days Battles as well as the Northern Virginia Campaign. As a brigade commander in the III Corps, General Carr participated in the battles of Fredericksburg and Chancellorsville (commanding a division during a part of the latter after the death of Hiram Berry).