In LostMagic the player controls Isaac, a young Wizard who initially sets out looking for his missing father. Soon his investigations uncover a threat to the world by the evil Diva of Twilight. In order to find his father and stop the Diva, he needs to travel the world to find the most powerful Wizards, free them from the Diva's control, and learn their secret techniques. By his side are another Wizard named Trista and an ever-growing army of monster allies Isaac can capture and tame.

LostMagic is a game whose primary focus is combat, with little in the way of exploration to interrupt the main theme of the game. The stylus is used to direct the player's units and to cast spells. Mission goals typically involve some combination of routing the enemy and capturing certain points on the map, and every mission is under a strict time limit. Some maps have out-of-the-way treasure chests that contain helpful equipment.

The focus of the game is capturing monsters to later help Isaac defeat the more powerful foes. Up to 400 different spells can be cast, many in combination with others to create new effects. The challenge lies in using the stylus quickly and accurately to not only combine these spells, but to effectively direct the real time battles. Each of these monsters and spells is tied to one of six elements.

The game supports Wi-Fi as well as both single and multi cartridge versions of multiplayer. Through Nintendo Wi-Fi Connection, players could be randomly matched up against one another in battle.