Fifth grader Chiyoko Kurotori, nicknamed Choco, has a strong interest in the occult and fortune-telling. While attempting to summon the love messenger Cupid to read her friends' love horoscopes, she has a stuffy nose and mispronounces the incantation. Instead of Cupid, she accidentally summons Gyubid, a beautiful but mischievous black witch. Rather than being angry, Gyubid decides to take Choco on as her apprentice, forcing her to begin training in the ways of black magic.

The story follows Choco as she tries to balance the normal life of an elementary school student with her secret, demanding magical studies. The training regimen from the self-proclaimed "hottest instructor of the magic world" is tough, and punishment for slacking is harsh. Aided by the fact that most people cannot see Gyubid, Choco must keep her extracurricular activities hidden from her classmates and teachers. Whenever she is involved in something pertaining to the occult, she is often required to wear a gothic lolita outfit.

The series is set primarily in Choco's school and hometown, where she faces off against various occult mysteries and magical mishaps. Her daily life is filled with comedic chaos as Gyubid, a trickster mentor who loves putting her student on the spot, frequently bungles situations or creates unintended consequences. Despite her tormenting nature, Gyubid does sincerely care for Choco's safety and will come to her rescue when truly needed.

The supporting cast includes Choco's friends from kindergarten, Meg Shion, and the class representative, Mai Ichiro. She also has a rival named Kyou Oogata, a former student whose magic was sealed but sometimes breaks free. Choco's grandmother, Chikako, is secretly very knowledgeable about the spirit world and was once a student at the Black Witch Public Academy herself before being expelled, a fact she keeps hidden to avoid intruding on her granddaughter's secret. Other recurring characters include Angolmois, a former classmate of Gyubid's who serves as her boss, and Gyubid's former junior, Tōka Blossom.

Notable narrative arcs involve Choco's gradual development of her magical abilities, her confrontations with rival magic users, and the appearances of figures from Gyubid's past. The series builds towards a deeper exploration of the Black Witch Public Academy and Choco's own surprising family connection to the magical world, all while maintaining a lighthearted, comedic tone focused on friendship and perseverance.