Botchan, or a young master, grows up in Tokyo as a reckless and rambunctious youth. His parents favor his older brother, and he is also not well regarded in the neighborhood, having a reputation as the local roughneck. When his parents die, Botchan takes money from the inheritance and goes to study physics. Upon graduating, he accepts a job teaching middle school mathematics, but his arrogance and quick temper immediately lead to clashes with the students and staff. Mischief by the students turns out to be just the first salvo in a broader web of intrigue and villainy. The school's head teacher (Red Shirt) and English teacher (Squash) are vying for the hand of the local beauty (Madonna), and two camps have formed within the middle school staff. Botchan aligns with Squash and the head mathematics teacher (Porcupine) while they start a fight against the system and plot against Red Shirt.
