Kimihiro Watanuki is a high school student plagued by yōkai, spirits with a strong attraction to him. The spirits are invisible to others and encounters with them are extremely troublesome. When he stumbles into a shop that grants wishes, however, events in his life promise to become more unusual.

The shop is owned by Yūko Ichihara, a mysterious and beautiful witch of many names and esoteric renown. For a price, she offers to grant Watanuki's wish to be rid of the spirits. The price, according to Yūko, must be of equal value and so, as payment, he temporarily becomes Yūko's part-time employee.

Watanuki's job consists of small errands dealing with the supernatural and household chores. His love interest, Himawari Kunogi, and "rival," Shizuka Dōmeki, occasionally join him in his work as per Yūko's request. The three become increasingly close despite Watanuki's annoyances with Dōmeki.