"Kocchi Muite Miko" centers around Miko, a young girl who works as a shrine maiden at her family's shrine. Her life takes an unexpected turn when she encounters a mischievous fox spirit named Kon, who claims to be a divine messenger. Kon's arrival disrupts Miko's daily routine, as the fox spirit often causes trouble with its playful and unpredictable behavior. Despite Kon's antics, Miko gradually forms a bond with the spirit, learning to navigate the challenges it brings while balancing her responsibilities at the shrine.

The series explores Miko's interactions with Kon and other supernatural entities that visit the shrine, blending slice-of-life moments with lighthearted comedy. Each episode typically features self-contained stories, often revolving around Miko's attempts to manage Kon's mischief or resolve issues caused by other spirits. The dynamic between Miko and Kon serves as the core of the narrative, with Miko's grounded personality contrasting Kon's chaotic energy.

Supporting characters include Miko's family members, who are aware of the supernatural occurrences but often leave Miko to handle them. The shrine itself becomes a focal point for various supernatural events, creating a setting where the mundane and the mystical intersect. The tone remains light and humorous, with occasional moments of warmth as Miko and Kon's relationship evolves. The series avoids heavy drama, instead focusing on the charm of its characters and their everyday adventures in a world where the spiritual and human realms coexist.