At Matatabi Kindergarten, in the Sumire class, a new teacher named Yamada Tamako has just started her job. She quickly discovers that her most energetic student is a four-year-old boy named Inumaru, who is always cheerful, always full of mischief, and almost always completely naked from the waist down. Inumaru has no sense of shame or social convention, and his unpredictable antics—running through the hallways, disrupting lessons, and baffling adults with his logic—constantly test the patience of the teachers and parents around him. Tamako, earnest and kindhearted, tries to maintain order while learning to understand and manage Inumaru's wild behavior, often finding herself caught between her duties and his chaos.

The series follows the daily life of the Sumire class, introducing a cast of memorable children who interact with Inumaru in various ways. There is Suzume, a gentle girl who becomes Inumaru's first crush and invites him on a date to the zoo; Futoshi, a friend whose family later moves away, marking an early moment of sadness and growth; and later, a wealthy boy named Takemochiyo, who arrives with his butler and disrupts the classroom dynamic. The story balances exaggerated, absurd comedy with occasional warm and sincere moments, as the children experience friendship, rivalry, and small adventures within the kindergarten setting.

Over the course of the series, the students of Sumire class eventually move up to the older class and later face graduation and separation. Inumaru's growth is subtle but present; while he retains his unique, carefree personality, he becomes a little more aware of the world around him. The final arc follows the children as they leave kindergarten behind, with Inumaru preparing for elementary school. He writes a message to his future self and steps forward into a new chapter of his life, carrying the memories of his time at Matatabi Kindergarten with him.