At the beginning of the American Civil War, Waring resigned from the Central Park project to accept a military commission as major. He departed New York in the early summer, and drilled for a month in Washington DC, occasionally meeting President Lincoln as he reviewed the troops. Waring departed Washington DC on July 4, 1862, and fought at Battle of Blackburn's Ford. He then joined John C. Frémont and headed to St. Louis, where he commanded the Fremont Hussars. His beloved mare Vixen died on campaign in November 1862, near Jefferson City.