The first mission objective was to dock with an Agena Target Vehicle, as had first been achieved on the Gemini 8 mission. The accomplishment was not possible because of a launch preparation error on the target vehicle.

A second objective was a planned extravehicular activity (EVA), or "space walk", by the right-hand seat Pilot. The plan was for him to move to the rear of the spacecraft and strap himself into the Air Force's Astronaut Maneuvering Unit (AMU), a 'rocket pack' that would allow the pilot controlled flight, independent of the capsule's life support system. Use of the AMU was not achieved due to Cernan experiencing high cardiac stress, overheating, and fatigue during EVA.

A third objective was to carry out seven scientific experiments, including a medical experiment that measured the astronauts' reactions to stress by measuring the intake and output of fluids before, during, and after the flight.