Negi Springfield, a ten-year-old wizard prodigy from Wales, graduates from the Merdiana Magic Academy and is sent to Japan to teach English at Mahora Academy as part of his training. His goal is to become a Magister Magi, a master wizard who bridges the magical and non-magical worlds. Assigned to Class 2-A, Negi quickly discovers that his students are a lively and diverse group of 31 girls, each with distinct personalities and quirks. Despite his young age, Negi strives to connect with his students while keeping his magical abilities a secret.

The narrative unfolds as Negi’s dual life as a teacher and wizard becomes increasingly complicated. Early on, he forms a pactio contract with Asuna Kagurazaka, one of his students, after accidentally revealing his magic during a confrontation. A pactio is a magical bond that grants the contractor unique abilities, and over time, Negi forms similar contracts with several other students, each unlocking their latent potential. These contracts become crucial as Negi and his class face various supernatural threats, including rival mages, ancient artifacts, and dangerous magical creatures.

As the story progresses, Negi learns more about his mysterious past, particularly the disappearance of his father, Nagi Springfield, a legendary wizard known as the "Thousand Master." This quest for answers leads Negi and his students on adventures that take them beyond Mahora Academy, including trips to magical realms and encounters with powerful adversaries. The series balances episodic school life humor with overarching plotlines involving magic, combat, and character development.

Key characters include Asuna Kagurazaka, a spirited and protective student who becomes Negi’s first ally; Konoka Konoe, a cheerful girl with ties to the magical world through her grandfather, the dean of Mahora Academy; and Evangeline A.K. McDowell, a centuries-old vampire and former enemy who becomes a reluctant mentor to Negi. The large ensemble cast ensures a wide range of interactions and dynamics, with each student contributing to the story in unique ways.

Themes of friendship, perseverance, and self-discovery are central to the narrative, as Negi and his students grow stronger together, both as individuals and as a team. The series blends elements of comedy, action, and fantasy, with a focus on the challenges of balancing ordinary life with extraordinary circumstances. By the end, Negi’s journey as a teacher and wizard intertwines with his quest to uncover the truth about his father, setting the stage for further adventures and revelations.