Kiitarō is a young boy expelled from his family home due to his exceptionally strong sixth sense, which allows him to perceive supernatural beings called youkai. This occurred after he entered a forbidden storehouse. Relocating to a separate dwelling expecting solitude, he instead discovered it already inhabited by Suzu, a protective zashiki-warashi spirit. Their cohabitation began, attracting various other folkloric entities.

His daily life involves constant interactions with these spirits. He converses with beings like Yuki Onna, endures disruptions such as an akaname licking his bath, and navigates living alongside Suzu, whom he finds impossible to dislike. Kiitarō exhibits a blend of occasional kindness and mischievous curiosity, sometimes leading to comedic situations involving spirits like Suzu or Yukimusume.

Beyond core spirits like the nurikabe and mokumokuren encountered early on, Kiitarō meets a wide range of youkai. This includes a kitsunemen no onna (also named Yōko), Yukimusume, her mother Yukihaha, minor spirits like tenome and nobiagari, and animal-like entities such as mouse spirits.

Documented in his visual diary, Kiitarō adapts resiliently to the constant spirit presence. While occasionally displaying frustration or acting as a "jerk kid," he gradually develops camaraderie and acceptance towards the surrounding youkai community. His journey involves learning about each spirit's unique traits and folklore origins, often incorporating educational snippets.