Born in 1840 in Canada, Doherty came to New York in 1860 where he was living when the American Civil War broke out. He enlisted in a 90-day militia unit and was assigned as a Private to Company A of the 71st New York Volunteers on April 20, 1861. Assigned to Colonel Ambrose Burnside's 2nd Brigade of Brigadier General David Hunter's 2nd Division, he was captured by the Confederates during the First Battle of Bull Run, the first major land battle of the American Civil War, fought on July 21, 1861, near Manassas, Virginia. While a prisoner, he made a daring escape. Ultimately, the 71st Regiment, along with Doherty, mustered out on August 9, 1861.