Pokémon of all kinds attend a school called Pokémon Gakuen, where they experience the ups and downs of daily student life. The series follows the comedic misadventures of various Pokémon in classroom settings, from lessons and homework to field trips, sports festivals, and school plays. Each four-panel gag strip is largely self-contained, with humor derived from the Pokémon's personalities and interactions in a school environment.

The manga is organized into different classes, each taught by a Pokémon teacher. Early volumes feature a class led by Pignite, with students including Snivy, Tepig, and Oshawott, alongside classmates such as Trubbish and Cubchoo. The school's principal is Garbodor. Later volumes introduce new classes focused on Pokémon from later game generations: a class taught by Decidueye (Fukusuro) with Alola starters, a class taught by Goodra (Numerugon) with Kalos Pokémon, a class taught by Toxtricity (Bachinkī) with Galar starters, and a class taught by Pawmot (Pāmot) with Paldea starters. The series thus offers a rotating cast of beloved Pokémon from each mainline game region, all placed in a school setting.

There is no overarching story or character development; instead, the manga relies on episodic, playful humor that pokes fun at both school life and the traits of the featured Pokémon. The tone is lighthearted and accessible, aimed at readers of all ages who enjoy seeing their favorite Pokémon in silly, everyday situations.