Based on the 2002 summer movie starring Freddy Prinze Jr. and Sarah Michelle Gellar, the Game Boy Advance version of Scooby-Doo is an adventure played from an isometric viewpoint. The Scooby Gang has been hired to solve the mystery of Spooky Island, a resort whose tenants are panicked by an apparition called the Ghoulish Guest.

As either Scooby or Shaggy, players initially explore the hotel looking for clues and hints from the various guests walking about. Talking to people reveals new objectives, such as finding three keys, draining the nearby pool, or meeting up with a specific character. Completing these tasks brings the Mystery, Inc. team one step closer to cracking the case.

As players explore their surroundings, which are detailed in an overhead map viewable from the menu screen, they will eventually confront monsters, puzzles, and other dangers. Certain situations call for the talents of specific characters, as each member of the Scooby Gang possesses distinct abilities to help overcome a problem or enemy.

Players can freely switch between the characters (after finding them) to take advantage of their traits. Velma can tiptoe past enemies and open locked chests, Scooby and Shaggy run quickly, Daphne uses her skills in karate, and Fred is the strongest of the group. Each character has health and stamina meters that diminish after taking damage or using special techniques, but a number of scattered power-ups can help replenish them.

The adventure also offers four mini-games, each of which can be played in a separate mode. Unlock the Chest involves rotating three rings so the same colors are aligned, while Repair the Pipes has players fitting together pipe pieces to drain water. The other two games are the maze-like Lights Out and note-matching game Musical Mayhem. Progress is automatically saved after completing an objective or moving to another Spooky Island locale.