The story of Madu Monogatari A takes place at a time between Madu Monogatari I and Madou Monogatari II. Arle, the heroine of the series, is a little girl who studies magic. One day, she goes into a forest, only to notice that something terrible happened to it and its inhabitants, the fairies. Is this the work of the archenemy, Satan-sama? That's what Arle has to find out!

Like most other Madou Monogatari games, it takes place in 3D maze-like dungeons, which you should explore, find treasures, and fight enemies. The turn-based, random battles are viewed from the same first-person perspective as the dungeon exploration. You fight using a variety of magic spells.