John J. Miller was born May 3, 1842 at Fayette, Howard County, Missouri. He was a graduate of the University of Nashville and the Western Military Institute. During the early years of the American Civil War, he served as a drill officer in the 2nd Division of the Missouri State Guard. He also attended St. Louis Medical College. On May 14, 1863, Captain Miller was captured by Union troops in St. Louis after being wounded in the leg. He remained at one of the city's prisons until May 20 when he was transferred to Alton, Illinois and later to Sandusky, Ohio. He arrived at Johnson's Island on June 9, 1863, where he remained imprisoned until his exchange on April 22, 1864. From May of 1864 to the end of the war he served as a surgeon's assistant at Camp Winder General Hospital in Richmond, Virginia. Following the war, he returned to St. Louis and practiced medicine.