Just after the start of the Civil War, Duryée raised a new regiment, the 5th New York Volunteers, in less than a week. He became its colonel on May 14, 1861. It was one of the several Zouave units that were formed in the mid-19th century. "Duryée's Zouaves", as they became known, fought at Big Bethel. Duryée was appointed brigadier general, on August 31, 1861, to rank from that date. President Abraham Lincoln submitted the nomination to the U.S. Senate on December 21, 1861, and the Senate confirmed the nomination on February 3, 1862. Duryée was given command of a brigade in the division under General James B. Ricketts. He later fought in the Battle of Cedar Mountain, Second Battle of Bull Run, and several others. At the Battle of Antietam, he succeeded Ricketts as division commander, when the latter was wounded. He was not afraid to be in the thick of the action; he was wounded at Second Bull Run, South Mountain, and Antietam.