Phantom Brave is a strategy RPG which takes place in the world of Ivoire. Ivoire consists of vast seas and numerous islands; it used to be a peaceful place, but an ancient (and powerful) force is now threatening life in the various lands. The character you control in the game is Marona, a 13 year old orphaned girl. Marona has the ability to communicate with phantoms, an ability that brings a lot of resentment from other people but will help her to head out into the world and solve the problems that are occurring. A phantom known as Ash acts as Marona's guardian; as the game progresses, other phantoms will join your party, each of which have different capabilities.

The game features a turn based combat system. During battles, Marona is able to attack enemies by herself, and she can also summon phantoms in her party to help out. To summon phantoms, you will need to confine them to an object on the screen (such as a rock or tree). Once confined to an object, you will then be able to control the phantom in battle, though phantoms only remain controllable for a limited number of turns. The object you confine a phantom to will affect it's abilities; for example, a rock may make a phantom stronger but move slower. By defeating enemies in battle you earn experience points allowing to level up and become more powerful.

The games story takes place in 20 episodes. Each episode features a unique goal to be completed before moving on. Between episodes you can visit your home on Phantom Island; here you can summon additional phantoms to join your party. Initially only a few types of phantoms can be summoned, but more become available as experience is gained. You may also replay already completed episodes or enter a random dungeon in order to level up your party and earn additional money to buy items.