John Reeves Pierce was born on 3 November 1906 in Cristóbal, Colón, Panama Canal Zone. He graduated from the United States Naval Academy in 1928. Following flight training and submarine instruction, he served on the submarine USS S-29 and studied marine engineering at the University of California. After serving on and , he assumed command of on 15 February 1941. Appointed Lieutenant Commander on 2 January 1942, on 22 June he took command of , a transport submarine, which participated with "Nautilus" in carrying out the Raid on Makin Island from 17 to 19 August.