One night, 14-year-old Madoka Kaname has a terrible nightmare - against the backdrop of a devastated city, she witnesses a girl fight a losing battle against a dreadful being lingering above, while a cat-like magical creature tells Madoka the only way to change such tragic outcome is for her to make a contract with him and become a magical girl.

The next day, the teen's dream seemingly becomes reality as the girl she saw in her dream - Homura - arrives at Mitakihara Middle School as a transfer student, mysteriously warning Madoka to stay just the way she is; but when later on she and her best friend Sayaka encounter the same cat-like magical creature from her dream - who introduces himself as Kyubey - the pair discovers that magical girls are real, and what's more, they can choose to become one. All they must do is sign a contract with Kyubey and agree to take on the duty to fight abstract beings called 'witches' that spread despair to the human world, and in return, each one of them will be granted any single wish they desire. However, as Homura's omen suggests, there might be far more to becoming a magical girl than Madoka and Sayaka realize...

Notes:
- Due to the 2011 Tōhoku earthquake and tsunami, the broadcasts of episodes 11 and 12 were delayed and were later aired as a double feature on April 21, 2011.