When the American Civil War began in 1861, Chapin chose to follow his home state and the Union cause. He was mustered into the Union Army on September 6 as a captain in the 44th New York Infantry Regiment. The 44th left New York on October 21, numbering 1,061 strong, and joined the Army of the Potomac. On January 2, 1862, Chapin was promoted to major, and he fought during the Peninsula Campaign in Virginia. On May 27 he was seriously wounded in the Battle of Hanover Court House, among the 86 casualties the 44th suffered in the fight. Chapin's performance there was praised by his commanding officer, Brig. Gen. John H. Martindale.