STS-47 was NASA's 50th Space Shuttle mission of the program, as well as the second mission of the Space Shuttle Endeavour. The mission mainly involved conducting experiments in life and material sciences inside Spacelab-J, a collaborative laboratory inside the shuttle's payload bay sponsored by NASA and the National Space Development Agency of Japan (NASDA). This mission carried Mamoru Mohri, the first Japanese astronaut aboard the shuttle, Mae Jemison, the first African-American woman to go to space, and the only married couple to fly together on the shuttle, Mark C. Lee and Jan Davis, which had been against NASA policy prior to this mission.

As female and male astronauts became more prominently integrated with the shuttle program, NASA enacted an unwritten rule that husband/wife couples would not be assigned to the same mission. However, when Lee and Davis's marriage became known to NASA officials in January 1991, the officials decided to keep the assignment as is, given that both crewmembers already had important roles within the upcoming mission. When asked at a NASA press conference if intimate activities would be taking place on the mission, Davis denied that possibility.

At the beginning of September, a problem with an oxygen line in the shuttle's main propulsion system was identified, however, it was resolved without forcing a postponement of the mission.

STS-47 launched from Pad 39B at 10:23:00 a.m. EDT on September 12, 1992, and was the first on-time mission without launch delays since STS-61-B in 1985.

The mission's primary payload was Spacelab-J — a joint mission between NASA and the National Space Development Agency of Japan (NASDA) — which used a crewed Spacelab module to conduct microgravity research in materials and life sciences. Like many previous missions, the international crew was divided into red and blue teams which would work in two 12-hour shifts for around-the-clock operations. Brown, Lee, and Mohri were assigned to the red team, and would conduct experiments while Apt, Davis, and Jemison, assigned to the blue team, would rest, and vice versa. As the mission commander, Gibson was free to work with both teams. Because of the 24-hour schedule, the crew wasn't sent any traditional wake-up calls by mission control.

Spacelab-J included 24 experiments in materials science and 20 life sciences experiments, the majority of which were sponsored by NASDA and NASA, while 2 were sponsored by collaborative civilian efforts. The Payload Crew Training Manager was Homer Hickam, who also worked during the mission as a Crew Interface Coordinator to talk to the crew during their science experiments and relay any concerns from the scientists on the ground.

Materials science investigations covered such fields as biotechnology, electronic materials, fluid dynamics and transport phenomena, glass and ceramics, metals and alloys, and acceleration measurements. Life sciences included experiments on human health, cell separation and biology, developmental biology, animal and human physiology and behavior, space radiation, and biological rhythms. Test subjects included the crew, Japanese koi fish (carp), cultured animal and plant cells, chicken embryos, fruit flies, fungi, plant seeds, frogs and frog eggs, and oriental hornets.

Jemison and Japanese astronaut Mamoru Mohri were trained to use the Autogenic Feedback Training Exercise (AFTE), a technique developed by Patricia S. Cowings that uses biofeedback and autogenic training to help patients monitor and control their physiology as a possible treatment for motion sickness, anxiety and stress-related disorders.