By 1861, Dorr was working in Massachusetts as a clerk when the Civil War broke out. He quickly enlisted as a private in the 13th Regiment of Massachusetts Volunteers, Company B. During his period of service he most notably fought in the Battle of Antietam in September 1862. He was severely wounded in the leg which forced him to leave from active combat. He later wrote he was glad to have fought in the battle, despite the injury, due to its significance in the war, writing the battle was “probably next to Gettysburg in its immediate importance.”