Elemental Battle Academy is a 3D game with elements of gunplay and melee combat. Players can choose from one of six female characters, each with powers a particular element, such as air, fire, light, and water. The game can be played in single-player Story Mode or Arcade Mode, or online with multiple players. Players can fight with the other female characters, choose their own weapons, and dress up the characters by purchasing clothes using gameplay-earned currency.
When in battle, players can choose to use their own weapons. They can also wield the ones located inside green boxes. The Elemental Attacks can also be used to inflict damage to enemies within a wide area; when used with the Elemental Burst mode, the damage will be greater. The characters also have their own spirit animals whose elemental abilities may be used during battle. With these elemental powers and abilities, the characters can turn common objects into deadly weapons. The characters can also use melee weapons (such as a spear or a sword) and pair these up with a firearm.
Aside from the basic movement controls using the WASD keys, Elemental Battle Academy also allows players to switch weapons, discard weapons, and take cover from attacks using a combination of keys and mouse controls. The space bar makes the character jump; pressing B makes the character pick up discarded weapons; and characters can take cover beside a wall when the player presses the Z key.