Battle Queen is all about fights between beautiful young women. In the beginning of the game the player is given the option to choose one of the three available fighters. Each one has an introduction story. Sayaka witnesses the murder of her father, a circus acrobat, by a witch known as Lavender; her story begins with a fight against her. Mai's and Mercedes' stories are one and the same; they are fighting for dominance in modern-day Japan, and fight each other in the first round of their stories.

Despite looking like a fighting game, Battle Queen is strategy-, not action-oriented. The fights are turn-based. The player can choose between different moves, including four kinds of attack, jump, defend, special attacks, etc. Special attacks can only be executed after performing a sufficient amount of other moves.

Each move is displayed as an anime-style image. The girls lose parts of their clothes when being hit. Defeating the opponent results in a sex scene.