The US agency said on Saturday that the former astronaut's death was due to complications following pneumonia. The agency didn't say where he died.
He said Young, a former Navy test pilot, was special.
Young was a man of many firsts: the only astronaut to fly in the Gemini, Apollo and space shuttle programs (and the first to command a shuttle flight); and the first to fly into space six times.
"Today, NASA and the world have lost a pioneer", Robert Lightfoot, NASA administrator, said in a statement.
In NASA's history, few astronauts were more accomplished than John Young. He was a stickler for safety, which benefited and exasperated Nasa officials.
Then, in 1966, he flew as Commander on Gemini 10, the first mission to rendezvous with two separate spacecrafts on the course of a single flight. "He was always questioning what we were doing and why we were doing it".
"Barbara and I join our fellow Americans and many friends in the space community in mourning the loss of astronaut John Young", Bush said in a statement.
He was part of the first manned Gemini mission - with Gus Grissom on Gemini 3 in 1965.
"John Young was at the forefront of human space exploration with his poise, talent, and tenacity", Lightfoot said.
His May 1969 Apollo 10 mission served as a "dress rehearsal" for the historic Apollo 11 mission two months later in which Neil Armstrong became the first person to walk on the moon. During that time, they performed rendezvous maneuvers with a pair of Agena target vehicles that were already in orbit.
"I thought returning safely to Earth sounded like a good idea", quips Young, who has stood on the Moon, driven 16 miles in a lunar rover and spent three nights on the lunar surface. According to media reports, Young smuggled a corned beef sandwich in his spacesuit, a move that didn't sit well with NASA staff in Houston who anxious about the crumbs.
He feared it would get him fired, Mr Young said.
In 1981, Young commanded the shuttle program's inaugural mission, orbiting Earth 37 times in the Columbia. Three years later he was selected as a NASA astronaut.
In his autobiography, he revealed that he felt responsible for the shuttle accidents of the Challenger (1986) and Columbia (2003).
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