Wagner enlisted in August 1861 with the 88th Pennsylvania Volunteer Infantry during the Civil War and was mustered in September 13, 1861, and commissioned 1st lieutenant of Company D. He rose to the rank of captain of Company D and was wounded in action at the Second Battle of Bull Run and captured, but paroled and recovered in hospital at Alexandria, Virginia; for his distinguished service during the battle, he was promoted to major of the regiment.

Wagner was wounded in action again at the Battle of Chancellorsville and returned to Philadelphia where he was recovering but deemed unfit for service in the field.

Upon a surgeon's recommendation, Wagner received the command and was detached from his regiment during the entire time that the camp was in operation.

Wagner was eventually promoted colonel and served as commander of the 5th Brigade, Pennsylvania National Guard until the war's end.

After the war, Wagner served as commissioner of public works for Philadelphia and was very active in the Grand Army of the Republic, both at the local, state, and national levels.