Little Witch Story is a work of interactive fiction. The game is set in a world similar to ours, except that scientists in that world have been able to confirm the existence of witchery, and can identify people with magical abilities using a simple DNA test. The discovery leads to discrimination against the witches, as public debate rages over whether they should be considered fully human and entitled to the same rights as everybody else. The story takes place in a high school, with the teenage protagonist unexpectedly discovering that they are a witch themselves. Now, their old friends are uneasy around them, their teachers treat them with suspicion, and to make matters worse, as soon as they become a part of the local magical community, they discover something strange is happening to the witches in the city.
Little Witch Story plays similarly to other interactive stories made with Twine, consisting of text with choices that can change the outcome of the story. There is a total of eight endings.The magical premise of the game is clearly intended as a metaphor for the LGBTQ community, and the game features a diverse and inclusive set of characters.