The Uncanny X-Men is an overhead-view action game. Players commence by selecting two X-Men from the roster, with the second controlled by another player or the computer. They then choose one of five levels, including a practice level. The objective in each level is to reach the concealed 'command centre' and demolish it. All X-Men share similar abilities, allowing movement in any direction, jumping, and attacking. Half of the characters (Storm, Iceman, Cyclops) possess long-range attacks, while the other half (Wolverine, Nightcrawler, Colossus) need to engage enemies in close combat. Each X-Man can endure a specific number of hits before being defeated. If both X-Men fall in battle, players can select two more to attempt the level again until all X-Men are used.

Power-ups include an "S" that stops time, temporary invincibility, and a health restore. Additionally, a Magnet power-down (symbolizing Magneto) temporarily immobilizes the X-Men.