He served as fire control officer on the destroyer until June 1953 and completed a tour in the Sea of Japan during the Korean War. Following this assignment, he was sent to flight training. In January 1954, he was designated a Navy helicopter pilot. After receiving his aviator wings on December 20, 1954, he was assigned to Fighter Squadron 103 (VF-103) for four years, flying Grumman F9F Cougars from and Vought F8U Crusaders from . After training at the United States Naval Test Pilot School in 1959 with the Class 23, Young was assigned to the Naval Air Test Center at Naval Air Station Patuxent River, Maryland, for three years. His test projects included evaluations of the XF8U-3 Crusader III and F-4 Phantom II fighter weapons systems. In 1962, he set two world time-to-climb records while flying his Phantom II, attaining from a standing start in 34.52 seconds and from a standing start in 227.6 seconds. He also served as maintenance officer of Fighter Squadron 143 (VF-143) from April to September 1962. Fellow astronaut Charles Bolden described Young and Robert "Hoot" Gibson as the two best pilots he had met during his aviation career: "Never met two people like them. Everyone else gets into an airplane; John and Hoot wear their airplane. They're just awesome". Young retired from the Navy as a Captain in September 1976, after 25 years. Joining NASA in 1962, Young was the first of the Astronaut Group 2 to fly in space, replacing Thomas P. Stafford as pilot of Gemini 3 when Alan Shepard, the original command pilot, was grounded due to Ménière's disease. Making the first crewed flight of the Gemini spacecraft with Gus Grissom in 1965, Young scored another space first by smuggling a corned beef sandwich onto the spacecraft—a feat for which he was reprimanded. Some members of the U.S. House of Representatives were not pleased about the stunt, claiming that Young cost taxpayers millions of dollars by disrupting a scheduled test of space food during the flight. Young then trained as backup pilot for Gemini 6A. The assignment of Gemini 7 backup command pilot Ed White to Apollo, created an opening for Young as commander of Gemini 10 in 1966. The mission was the first to perform a rendezvous with two Agena target vehicles; and his pilot, Michael Collins, performed two spacewalks. In 1966, Young was assigned to an Apollo crew as Command Module pilot, with Commander Thomas Stafford and Lunar Module pilot Eugene Cernan.