Born either in Brightstown, New York or Philadelphia, Pennsylvania, Allen enlisted as a private into the 29th Pennsylvania Volunteers on August 15, 1864, and served through Sherman's March to the Sea, until June 7, 1865. In August 1865, he enlisted in the Regular Army at Lansingburgh, New York and was assigned to the 23rd U.S. Infantry. Eventually reaching the rank of first sergeant, he was part of the Lieutenant Colonel George Crook's campaign against the Apache during the early 1870s. On March 27, 1873, he took part in a major engagement against the Yavapai Apaches at Turret Peak, Arizona, only 20 miles south of Camp Verde. He, along with Captain George M. Randall, led a successful surprise attack and was awarded the Medal of Honor for "gallantry in action". He officially received the medal on April 12, 1875, two years after the battle.