Negi Springfield, a ten-year-old prodigy and aspiring wizard from Wales, graduates from the Merdiana Magical Academy and is sent to Japan to teach English at Mahora Academy as part of his training. Despite his young age, Negi is determined to prove himself as both a teacher and a mage. His class, 2-A, consists of 31 female students, each with distinct personalities and backgrounds. Early in the story, Negi accidentally reveals his magical abilities to one of his students, Asuna Kagurazaka, who becomes his partner and confidante. This discovery sets off a chain of events that intertwines the mundane world with the magical one.

As Negi settles into his role, he learns that his father, Nagi Springfield, a legendary mage known as the "Thousand Master," disappeared years ago under mysterious circumstances. Negi’s journey becomes a quest to uncover the truth about his father’s fate while honing his magical skills. Along the way, he forms pacts with several of his students, granting them magical abilities and transforming them into his allies. These pacts, known as "Magister Magi" contracts, deepen the bonds between Negi and his students, creating a team capable of facing increasingly dangerous threats.

The narrative explores a mix of slice-of-life school scenarios and high-stakes magical conflicts. Early arcs focus on Negi’s efforts to balance his teaching responsibilities with his magical training, often involving comedic misunderstandings and lighthearted interactions with his students. However, the tone gradually shifts as darker elements emerge. The class becomes entangled in battles against powerful magical entities, including the enigmatic "Fate Averruncus," a mage with ties to Negi’s father, and the sinister "Cosmo Entelecheia," an organization seeking to manipulate magical and technological forces for their own ends.

Key characters include Asuna, whose cheerful and protective nature contrasts with her hidden past and latent magical potential; Konoka Konoe, a kind-hearted girl with ties to the magical world through her grandfather, the dean of Mahora Academy; and Setsuna Sakurazaki, a skilled swordswoman and Konoka’s devoted protector. Other students, such as the mischievous Evangeline A.K. McDowell, a vampire mage with a complex history, and Nodoka Miyazaki, a shy bookworm with a unique magical ability, play significant roles in Negi’s journey.

The story delves into themes of friendship, responsibility, and the struggle between duty and personal desires. As Negi grows stronger, he faces moral dilemmas and the consequences of his actions, particularly as his quest to find his father intersects with larger conflicts involving the fate of both the magical and non-magical worlds. The series blends action, humor, and emotional depth, culminating in a climactic battle that tests the limits of Negi’s abilities and resolve. Through his experiences, Negi evolves from a naive child into a capable leader, leaving a lasting impact on his students and the world around him.