Botchan, the nickname given to the narrator by his motherly caretaker Kiyo, is the only name we are given for our protagonist. He is a self-described trouble maker who, after graduating from a School of Physical Sciences in Tokyo, takes a job as a math teacher in a rural town on an island off Japan. He will make 40 yen a month. After his first day in school the Porcupine (the nickname Botchan gives to his fellow math teacher) helps him find a place to live.

Botchan finds teaching to be more difficult than he envisioned, and the students do not entirely respect him. After he is seen frequenting noodle and dumpling shops, the students mock him with notes on the chalkboard about how many pieces of tempura he ate. He is also mocked for his temper and for swimming in the hot springs.

One day Redshirt (the assistant principal) and the Hanger-On (Redshirt's lackey) invite him to go fishing. Though he doesn't fish much, Botchan enjoys the relaxing day until the end, when Redshirt implies that he should be careful because if he trusts the wrong kind of person, he could end up getting in trouble, or even fired. Redshirt implies that the Porcupine has it out for Botchan. Botchan also overhears on this trip something about the Madonna, who he assumes is a woman Redshirt is interested in. The next day Botchan confronts the Porcupine, and they have a fight, the result of which is the two quit speaking and Botchan is forced to find new living arrangements.

The Pale Squash (another teacher) helps Botchan find a new place to live. Botchan's new landlady shares some gossip with Botchan that helps him understand that the Madonna was engaged to the Pale Squash, but Redshirt has been attempting to break the engagement off so he can marry her, but his efforts are very subtle. The Badger (the principal) announces at school that the teachers can no longer go to noodle or dumpling houses.

The fight between Botchan and the Porcupine eventually ends, when Botchan realizes that Redshirt is the bad guy, and not the Porcupine. The Porcupine also discovers the landlord he helped Botchan live with was lying about the things Botchan did. The Pale Squash is tricked by Redshirt into moving to a distant village to teach, officially ending the engagement to the Madonna.

During a celebration of a war victory, The Porcupine and Botchan try to break up a fight among students, but end up getting involved. The event is reported in the newspaper and a few days later the Badger and Redshirt force the Porcupine to resign. Botchan threatens to resign as well, since he was as much involved as the Porcupine. He doesn't immediately, however, as the Porcupine devises a plan to catch Redshirt with a geisha. Over a week passes, but eventually they catch Redshirt and the Hanger-On in the act. Botchan and the Porcupine beat up the two men to teach them a lesson. Botchan resigns and returns to Tokyo, where he gets a house for him and Kiyo. The two live together for just a short time before she dies from pneumonia.