WipEout Fusion is a futuristic racing game with action elements. Playing compete in the F9000 Anti-Gravity Race League, driving hovercrafts and sometimes using weapons against opponents to achieve victory.

Like WipEout 3, the game contains single-race and league modes, as well as two-player split screen gameplay. The single race mode (called Arcade) is used to unlock new tracks. The challenge mode from WipEout 64 returns with a few enhancements: each team has its own set of six challenges, which must be completed with a medal in order to unlock the next one. A new Zone mode requires players to drive as many loops as possible on a track while continuously increasing the speed.

Another new feature in WipEout Fusion are hovercraft upgrades. Depending on their performance, players receive credits after races, which can be used to increase speed, thrust, weapon power, shield strength, lateral stability, and brake force of a vehicle. Upgraded vehicles can be used in any other game mode, with the exception of the Challenge mode.