Launch from Cape Canaveral; landing 1010 km southwest of the Bermuda Islands.

The launch was successful after the third attempt. This mission was originally intended to be the first mission to dock with an Agena Target Vehicle, but the Agena exploded 6 minutes after its launch on October 25, 1965 and the mission was cancelled. The plans were changed then. Now the main goal was a rendezvous of two Gemini spacecrafts in space. The flight schedule was changed too, now the next mission was Gemini 7 and Gemini 6 was now named Gemini 6A.

But the second launch attempt on December 12, 1965 also failed. The Titan rocket shut down on the pad. The problem was, that the instruments had shown already a launch, when the engines shut down, so normally the crew had to eject. But Walter Schirra didn't with the simple reason, that he didn't felt any motions of the capsule (from which it could have fallen down and exploding). He trusted his senses and that was correct. When the engineers examined the thrust versus time graph, they found that the thrust rose nominally but started to get lower before the plug had fallen out. Through the night, engineers examined the rocket engine piece by piece until they found that a plastic cover had been left in the gas generator port. With this problem solved the rocket and spacecraft were recycled for a launch 72 hours after the first attempt.

The third attempt then was successful and the rendezvous maneuver with the earlier launched spacecraft Gemini 7 too. During 270 minutes the crews moved as close as 30 centimetres to 90 meters, talking over the radio, while Gemini 7 almost drifted and Gemini 6A made the burns, because they had more fuel. It was the first radar contact between the two spacecraft.

The rendezvous maneuver was the only work to do. The flight ended with a nominal reentry and landing in the West Atlantic, just 10 km from the planned landing point. The recovery ship was the USS Wasp. It was the first successfully controlled reentry and they did in full view of live television beamed from the Wasp via satellite transmission.