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NASA career
In 1962, NASA needed a second group of astronauts for the Gemini and Apollo programs. Lovell applied again, and this time was accepted into NASA Astronaut Group 2, as was Conrad.

Gemini program
Lovell was selected as backup Pilot for Gemini 4, which put him in position for his first space flight three missions later as Pilot of Gemini 7 with Command Pilot Frank Borman in December 1965. This flight set an endurance record of fourteen days in space, and also was the target vehicle for the first space rendezvous with Gemini 6A.

Lovell was later scheduled to be the backup Command Pilot of Gemini 10, but after the deaths of the Gemini 9 prime crew Elliot See and Charles Bassett, he replaced Thomas P. Stafford as backup commander of Gemini 9A. This again positioned Lovell for his second flight and first command, of Gemini 12 in November 1966 with Pilot Buzz Aldrin.

Lovell's two Gemini flights gave him more time in space than any other person as of 1966.

Apollo 8
Lovell was originally chosen as Command Module Pilot on the backup crew for Apollo 9, planned as a medium Earth orbit test of the Lunar Module, along with Neil Armstrong as Commander and Buzz Aldrin as Lunar Module Pilot. Lovell later replaced Michael Collins as CMP on the Apollo 9 prime crew, reuniting him with his Gemini 7 commander Frank Borman, and LM pilot William Anders, when Collins needed to have surgery for a bone spur on his spine.

But then, delays in construction of the first manned LM prevented it from being ready in time to fly on Apollo 8, planned as a low Earth orbit test. It was decided to swap the Apollo 8 and Apollo 9 prime and backup crews in the flight schedule so that the crew trained for the low-orbit test could fly it as Apollo 9, when the LM would be ready. The original Apollo 9 medium Earth orbit test was replaced with a lunar orbital flight, now Apollo 8. Borman, Lovell and Anders were launched on December 21, 1968, becoming the first men to travel to the Moon.

As CM Pilot, Lovell served as the navigator, using the spacecraft's built-in sextant to determine its position by measuring star positions. This information was then used to calculate required mid-course corrections. The craft entered lunar orbit on Christmas Eve and made a total of ten orbits, most of them circular at an altitude of approximately 70 mi for a total of twenty hours. They broadcast black-and-white television pictures of the lunar surface back to Earth, and Lovell took his turn with Borman and Anders in reading a passage from the Biblical creation story in the Book of Genesis.

They began their return to Earth on Christmas Day with a rocket burn made on the Moon's far side, out of radio contact with Earth. (For this reason, the lunar orbit insertion and trans-Earth injection burns were the two most tense moments of this first lunar mission.) When contact was re-established, Lovell was the first to announce the good news, "Please be informed, there is a Santa Claus." The crew splashed down safely on Earth December 27.

Apollo 13
Lovell was backup commander of Apollo 11 and was scheduled to command Apollo 14, but he and his crew swapped missions with the crew of Apollo 13, as it was felt the commander of the other crew, Alan Shepard, needed more time to train after having been grounded for a long period. Lovell lifted off aboard Apollo 13 on April 11, 1970 with CM Pilot Jack Swigert and LM Pilot Fred Haise. He and Haise were to land on the Moon.

But on April 13, while in Earth-Moon transit, a damaged heater coil in a cryogenic oxygen tank sparked during a routine tank stir. This quickly turned liquid oxygen into gas with a huge increase in pressure, which burst the tank and damaged a second tank, resulting in the loss of all stored oxygen in just over two hours. This disabled the fuel cell-driven electrical power system, crippling the Command/Service Module "Odyssey" and requiring immediate abort of the landing mission; the goal of the mission became safely returning to Earth.

Using the LM as a "life boat" providing power, oxygen and propulsion, Lovell and his crew immediately re-established the free return trajectory which they had left, and swung around the Moon to return home. Based on calculations made on Earth, Lovell had to adjust the course two times by manually controlling the Lunar Module's thrusters and engine, using his watch for timing. Apollo 13 returned safely to Earth on April 17. Lovell is one of only three men to travel to the Moon twice, but unlike John Young and Eugene Cernan, he never walked on it.

His combined Gemini and Apollo flights made him the record holder for time in space (over 715 hours) and he had seen more sunrises from space than any human who had ever lived until the Skylab missions. It is also probable that Apollo 13's flight trajectory gives Lovell, Haise, and Swigert the record for the farthest distance that humans have ever travelled from Earth.