In Joggernauts, players take turns switching to the head of a jogging team of alien athletes as they navigate through deceptively difficult color-coded platforming levels while avoiding crashing into obstacles. In order to finish the level and collect all the trophies for victory, teams must work together and time their jumps and switches perfectly.

Players can also take on the challenges by themselves in the uniquely designed singleplayer mode, where one player simultaneously controls two different colored characters. Friends can also hot swap in to partake in two to four person co-op play. While jogging, players must switch the corresponding color to the front of the line of characters in order to match the color of enemies, obstacles, prizes and pickups in the level. Failure to do so can result in dreaded death, which reduces the overall shared number of lives for the team. Players always succeed or fail as a group, either successfully crossing the finish line, or failing and restarting the level, together.