 Van Vliet was promoted to major on August 3, 1861, and Brigadier General, Volunteers, on September 23, 1861.During the Civil War, he was chief quartermaster of the Army of the Potomac from August 1861 until July 10, 1862.His appointment to brigadier general expired a week later, and he was stationed in New York City for the remainder of the war, coordinating supplies and transportation for troops in the field.