A ten year old boy from Wales named Negi Springfield has just graduated at the top of his class from a magic school. To complete his training as a wizard, he is sent to Japan to serve as an intern teacher at the prestigious Mahora Academy, a massive university town. His assignment is to be the homeroom teacher of a middle school class of thirty one girls, each with a distinct and challenging personality. He must keep his magical abilities a secret from the public while navigating the chaos of a classroom.

Accompanied by his stoat familiar, Chamomile, Negi immediately struggles to control his rambunctious students. One of the most active and headstrong students, Asuna Kagurazaka, discovers his secret. Initially antagonistic toward the boy who replaced a teacher she admired, Asuna eventually agrees to keep his secret, and the two form an unlikely partnership. However, they soon face a greater threat within their own classroom. Another student, Evangeline, is revealed to be a powerful and ancient vampire mage who becomes suspicious of Negi. This conflict forces Negi and Asuna to work together in battle, leading Negi to form a magical pactio contract with Asuna, temporarily granting her magical abilities. This marks the beginning of Negi's maturation, both as a teacher and as a mage, as he follows in the footsteps of his legendary missing father, the "Thousand Master" Nagi Springfield.

The series follows Negi as he navigates numerous school-related incidents that often escalate into magical duels. The narrative includes a school trip to Kyoto, where Negi delivers a letter to the Kansai Magic Association and faces new enemies targeting one of his students, Konoka Konoe. This arc explores the relationship between Konoka and her bodyguard, Setsuna Sakurazaki, revealing deeper magical conspiracies. As the story progresses, Negi must deal with Evangeline’s schemes to steal his power, search for clues about his father's past, and protect his class from external magical threats. Throughout these adventures, he slowly earns the trust and affection of his students, several of whom form their own pactio contracts with him to help in battle.