It follows the adventures of female middle school students who became magical girls in exchange of their wishes to be granted and must fight against witches while learning the anguish and perils of their roles.

It all started when Madoka Kaname and Sayaka Miki meet Kyubey, a small white cat-like creature with long fluffy tail and circle red eyes offered contract to obtain those magical powers. Madoka has short pigtailed pink hair, pink eyes, wears brown longsleeve blouse with red ribbon tie, checkered short skirt, thigh-high socks, and dark brown shoes. Her magical attire consists of short-sleeved corset-like top pink and white dress with bell-shaped skirt, knee-high boots, and red heels with red bow. Sayaka, has chin-length blue hair, blue eyes, wears blue outfits; a tube top with blue symmetrical sort skirt, white cape, thigh-high socks, and blue booties.

They were stopped by Homura Akemi, a transfer student with long black hair with bangs and black plain headband, wears a uniform-like top, short skirt, black pantyhose with diamond boxes revealing his side legs, and black shoes. And then met Mami Tomoe, an upperclassman having blonde hair with curly pigtails tied on the back of the ears, wears bodyfit outfit with brown skirt, and black thigh-high socks under a knee-high boots.

Madoka saw how the witches killed Mami and discovered that when their source of magic, Soul Gems too tainted with despair, will turn into witch. She saw this when Sayaka, her friend turn into witch. And later she learned that Homura was a magical girl trying to save them from grisly fate.