He was 87 and died late Friday of complications from pneumonia, the space agency said. He lived in a Houston suburb just minutes from the NASA Space Center.
"NASA and the world have lost a pioneer," agency administrator Robert Lightfoot said in a statement. "We will stand on his shoulders as we look toward the next human frontier."
Young was a man of many firsts: the only astronaut to fly in the Gemini, Apollo and space shuttle programmes (and the first to command a shuttle flight); and the first to fly into space six times.
Young joined Gus Grissom on the Gemini 3 mission, then commanded the first space shuttle mission in what some people called "the boldest test flight in history."
He commanded Gemini 10, the first mission to rendezvous with two other spacecraft during a single flight.
Young orbited the moon in Apollo 10, and made a lunar landing with Apollo 16. "In an iconic display of test pilot 'cool,' he landed the space shuttle (STS-9) with a fire in the back end," NASA said.
"He was in every way the 'astronaut's astronaut,'" Lightfoot said. But he was also described as a savvy engineer and a "test pilot's test pilot."
Once, during an air-to-air missile test, Young and another pilot approached each other's aircraft at a potentially calamitous speed of Mach 3 (2,300 miles per hour, or 3,700 kilometers per hour), according to Young's website.
"I got a telegram from the chief of naval operations," Young said in his understated way, "asking me not to do this any more."
Fellow astronaut Charles Bolden called Young and Robert "Hoot" Gibson the two best pilots he had ever known.
"Never met two people like them," he said. "Everyone else gets into an airplane; John and Hoot wear their airplane. They're just awesome.
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