Launch from Cape Canaveral; landing 620 km southwest of the Bermuda-Islands in the Atlantic Ocean.

Launch was scrubbed because of a spacecraft computer malfunction, which ended in a hold of the countdown, and then thunderstorms approached the Cape Canaveral area. With the computer problem unresolved and the weather deteriorating rapidly, the mission was completely scrubbed and rescheduled for August 21, 1965.

No problems during the first two orbits and the ejection of the (REP). It was planned to evaluate the performance of the rendezvous guidance and navigation system, but then the pressure in the oxygen supply tank of the fuel cell system dropped down. The spacecraft was powered down and the REP exercise was abandoned. Even a premature end of the mission was considered. But the powering up of the fuel cells was successful and the mission could continue. On Mission day 3 a simulated Agena rendezvous with four different maneuvers was conducted at full electrical load, using the orbit attitude and maneuver system (OAMS). In the following days several thrusters failed, so the experimental and operational activities continued, but were limited. Only a few onboard medical tests were continued (the same as Gemini 4) to show the feasibility of longer flights and photographical work. Seventeen experiments had been planned (one was cancelled). But all in all in was a little bit boring and Conrad later lamented, that he had no book to read. The main goal was now only, to have a new flight duration record, which was successful. While Gemini 5 drifted, the cabin got cold.

Because of the erratic, and sometimes inoperable, OAMS, the crew was allowed to use one of the two rings of the reentry control system to position the spacecraft properly more than one revolution before coming back to Earth. Due to a computing error (wrong programming), the crew landed 130 kilometers short of the planned landing point. The short landing caused no problems for the U.S. Navy recovery forces. There were several carrier in the landing area. A helicopter (from USS DuPont) soon arrived and the crew was brought to the USS Lake Champlain.