Phantom Brave is a tactical role-playing game with battles that take place on an isometric board. Marona dispatches her phantom allies by confining them to objects on the field, such as trees, grass, rocks, and flowers. Different objects grant different stat bonuses to the characters that are confined to them, making it advantageous to confine certain characters to certain things. A soldier, for example, often benefits from the stat bonuses found on a rock because of his physical combat abilities, whereas a witch works better when summoned out of a flower or another object that increases its magical abilities. Up to 14 phantoms can be dispatched during any given battle, but the phantoms can only be confined to the physical world for a particular number of turns. The number of turns that a character can stay confined is based upon their class. For example, a witch can stay on the field for three turns, while a soldier lasts eight. While a high confine is desirable for continuous use of the character, a low confine number is actually advantageous if the player intends to either reuse the item to confine another phantom or take items back from the battlefield permanently, or for bomber units. Depending on their class, each phantom has a certain chance of acquiring the item he is confined to, bringing it back to Phantom Isle when the battle is won.
Phantom Brave has a gridless system in which each character can move a certain number of dm in each turn. The terrain also has traction and pliability characteristics, which affect how long characters continue to slide along after they stop moving and how high they bounce when the character jumps down from a ledge. On slippery surfaces, it is possible to make the characters "ice skate" by moving very short distances (consuming few dm) and letting them slide to their destination. In addition, the hold and throw system inherited from Disgaea: Hour of Darkness allows characters to pick up and throw objects and even other characters (including allies) toward a desired location.
Unlike most tactical role-playing games, the border of the battle maps do not have barriers around their edges. Most characters and objects can be thrown off, hit off, fall off, or slip off of the field of battle and sent O.B. (out-of-bounds). Characters and objects that are O.B.'d are gone for the rest of the battle. When an enemy is O.B'd, the level of each of the remaining enemies rises by one, so the player can trade a large force of weak enemies for a smaller number of stronger ones. If the enemy's HP is reduced to zero before it is thrown out of the stage, its allies will not be granted a level up. The last enemy on the map cannot be thrown O.B., and Marona's team members do not gain levels for falling out of bounds.
All characters and weapons accumulate "mana" (a magical currency for increasing a character or weapon's abilities) whenever they kill an enemy. This mana can be spent to fuse two characters together, an item into a character, or an item to an item. Fusion increases the level cap of the beneficiary by the level of the consumed item or character. By spending mana, the player can improve equipment percentages (stat bonuses given to characters who equip the item or character) and confine percentages (bonuses to characters confined in the item on the field), and even transfer skills to the beneficiary. In Phantom Brave, weapons have a much greater effect on a character's stats than their natural affinity. The maximum obtainable character level is 9999.
While on Phantom Isle, a character class called Dungeon Monk can be asked to create a random dungeon. Some characteristics of the dungeon can be seen before creation, including the type and general number of enemies present, the floor conditions, and if the use of equipped weapons is restricted or not. Dungeons also have titles, which are applied to every enemy in the dungeon. As the floors of the dungeon are cleared, the title of the dungeon will improve. These titles can later be removed and placed on player characters or weapons to alter their stats. Random dungeons can also be retitled. A popular leveling trick is to give a random dungeon the "failure" title, allowing the player to beat hordes of high level enemies easily. Random dungeons tend to take the form of a linear series of floors, although occasionally a floor may have a special named layout (for example, "Self-Styled God" floors have a stronger enemy in the center of a terraced layout). These floors occur randomly and confer an extra bonus upon completion. Unlike in Disgaea, where to descend to the next floor one may merely move a character to a certain panel, in Phantom Brave one must defeat all the enemies present to continue. To leave a random dungeon, one must either clear every floor, or use a Dungeon Monk's Return skill, which costs money proportional to the current depth.
While between battles, Marona can return to her home; Phantom Island, where she can summon (create) new phantoms to aid her in future battles. The player starts off by being able to create characters from a limited selection of classes, but each class of enemy that is defeated in battle is added to the selection of phantoms the player may summon. Summoning phantoms requires only a nominal fee, but new phantoms always join at level 1 no matter when they are summoned. Marona's phantoms populate the island, and the player can converse with them. Many classes have a special utility on the island; Merchants sell items, Healers can recover the damage that units have sustained Fusionists can combine characters and items, Witches allow the player to reorder a character or weapon's spells and skills, and Blacksmiths combine mana with weapons to either level them up or to awaken latent skills hidden in the weapon. Phantom Isle hides several secret items and character classes, such as the Changebook, which allows the player to switch the character they explore the map with.
Phantom Brave has a series of extra maps following the main storyline. These post-game maps offer more powerful enemies and feature cameos by some members of the cast of the Disgaea games as enemies. After defeating these characters they will join the player's pool of playable characters as "phantom doubles". While the first couple of extra maps can be completed immediately after the main story, the later extra maps are very difficult and require a large amount of time invested into the game to be spent leveling characters and fusing weapons before they can be completed.