Final Fantasy Fables: Chocobo's Dungeon, tells the story of two Final Fantasy regulars, who now have become treasure hunters, Cid and Chocobo, as they are magically transported to a town where the townspeople's memories are being stolen by the ringing of a clock tower. There they find a boy named Raffaello, who is immune to the memory loss, and find out he has stored the townspeople's memories safely in a series of dungeons. The boy enlists Cid and Chocobo to retrieve these memories and return them to the people.
The gameplay mostly consists of exploring dungeons and defeating enemies and bosses in battles to earn experience points and leveling up. Not only does the game feature exploration, but also a job system, where players can do chores for job classes such as black mages, knights and scholars. Completing these tasks will earn these jobs skills to fight the enemies throughout the dungeons in the games. Players can also unlock job classes and special dungeons by collecting letters scattered throughout the dungeons, once they spell out a phrase for that speciality it will be unlocked.
Players can also fight against each other using the Nintendo Wi-Fi connection in card battles reminiscent of Yu-Gi-Oh!. Players can also play mini-games solo in the "Mog House", that utilizes the Wii Remote.