After working for Bell Labs on the radio inertial guidance system of the Titan I intercontinental ballistic missile, he was hired by NASA in 1961.

As Deputy Director of NASA's Office of Manned Space Flight, and later as head of the Apollo Spacecraft Program Office, Shea played a key role in shaping the course of the Apollo program, helping to lead NASA to the decision in favor of lunar orbit rendezvous and supporting "all up" testing of the Saturn V rocket.

While Shea served as a consultant for NASA on the redesign of the International Space Station in 1993, he was forced to resign from the position due to health issues.

Known for his quick intellect, he also endeared himself to his subordinates through small eccentricities such as his fondness for bad puns and habit of wearing red socks to important meetings.

[6] In 1961 he was offered and accepted a position with Space Technology Laboratories, a division of TRW Inc., where he continued to work on ballistic missile systems.

[4][7] In December 1961, NASA invited Shea to interview for the position of deputy director of the Office of Manned Space Flight (OMSF).

D. Brainerd Holmes, Director of the OMSF, had been searching for a deputy who could offer expertise in systems engineering, someone with the technical abilities to supervise the Apollo program as a whole.

"[6] When Shea was hired by NASA, President John F. Kennedy's commitment to landing men on the Moon was still only seven months old, and many of the major decisions that shaped the Apollo program were yet to be made.

[9] In November 1961, John Houbolt had sent a paper advocating lunar orbit rendezvous (LOR) to Robert Seamans, the deputy administrator of NASA.

While he began with a mild preference for earth orbit rendezvous, Shea "prided himself", according to space historians Murray and Cox, "on going wherever the data took him".

[11] In this case, the data took him to NASA's Langley Research Center in Hampton, Virginia, where he met with John Houbolt and with the Space Task Group, and became convinced that LOR was an option worth considering.

Relations between the centers were not good, and it was a major milestone in the progress of the Apollo program when von Braun and his team finally came to accept the superiority of the LOR concept.

Space historian James Hansen concludes that Shea "played a major role in supporting Houbolt's ideas and making the ... decision in favor of LOR",[12] while his former colleague George Mueller writes that "it is a tribute to Joe's logic and leadership that he was able to build a consensus within the centers at a time when they were autonomous.

"[13] During his time at the OMSF, Shea helped to resolve many of the other inevitable engineering debates and conflicts that cropped up during the development of the Apollo spacecraft.

Although technically a demotion, this new position gave Shea the responsibility for managing the design and construction of the Apollo command and lunar modules.

[16] He kept control of the program using a management tool that he devised for himself—a looseleaf notebook, more than a hundred pages in length, that would be put together for him every week summarizing all of the important developments that had taken place and decisions that needed to be made.

Presented with the notebook on Thursday evenings, Shea would study and annotate it over the weekend and return to work with new questions, instructions, and decisions.

While Shea blamed North American's management for the continuing difficulties in the development of the command module, project leader Harrison Storms felt that NASA itself was far from blameless.

Not having been at Langley with the Space Task Group, he was considered an "outsider" by men such as flight director Chris Kraft, who recalled that "the animosity between my people and Shea's was intense".

He became deeply involved in supporting George Mueller's effort to impose the idea of "all up" testing of the Saturn V rocket on the unwilling engineers at Marshall.

"[24] Shea's work also won wider attention, bringing him public recognition that approached that accorded to Wernher von Braun or Chris Kraft.

"[26]Although the spacecraft passed its review, the crew finished the meeting by presenting Shea with a picture of the three of them seated around a model of the capsule, heads bowed in prayer.

[32] Named to the advisory group chosen to support the review board,[33] Shea threw himself into the investigation, working eighty-hour weeks.

[34] Although the precise source of ignition was never found, it soon became clear that an electrical short somewhere in the command module had started the fire, probably sparked by a chafed wire.

Senator Walter Mondale had accused NASA engineers of "criminal negligence" with regard to the design and construction of the Apollo command module, and it was expected that Shea would be in the firing line.

In March, Webb sent Robert Seamans and Charles Berry, NASA's head physician, to speak with Shea and ask him to take an extended voluntary leave of absence.

On April 7 it was announced that Shea would be transferred to NASA headquarters in Washington, D.C. to serve as George Mueller's deputy in the Office of Manned Space Flight.

When Shea's reassignment was announced, one of his friends gave an anonymous interview to Time magazine in which he said that "if Joe stays in Washington, it'll be a promotion.

[7] In February 1993, NASA administrator Daniel Goldin appointed Shea to the chairmanship of a technical review board convened to oversee the redesign of the troubled International Space Station.

However, The Scientist offered a different interpretation, quoting sources who speculated that the bluntness of his speech, including criticisms of Goldin, may have been controversial in NASA circles.