He was commissioned first lieutenant of Company D, 2nd Vermont Infantry, on May 20, 1861, but resigned on November 5, 1861, for medical reasons. He rejoined his father's business, and returned to the Washington area, selling drugs to sutlers and military surgeons. He then accepted a position as major of the 10th Vermont Infantry on August 26, 1862. He was promoted to lieutenant colonel on October 17, 1862, and assumed command of the regiment as colonel on April 26, 1864, replacing Albert B. Jewett, who had resigned. He commanded his regiment at the battles of the Wilderness, Spotsylvania, North Anna, Totopotomy Creek, Cold Harbor, and Cedar Creek.