Hyōtenka no Kanojo ni Nanika Yōkai is a spin-off prequel that follows Hanabi Fukuzumi and Hyōka Shiroishi during their high school years at an all-girls school. Hanabi is a human who has an intense fear of youkai, while Hyōka is a snow youkai who has never had a friend. Their respective childhood companions, Akira and Tōji, arrange for the two to meet in the hope that they can help each other overcome their respective problems. From their very first encounter, Hanabi and Hyōka clash and argue, but over time they develop an abrasive yet genuine friendship that resembles a rivalry.

The story takes a turn when Hanabi meets Hyōka's younger sister, Hyōkei. Hyōkei is in love with a human named Sairyū and wishes to become human herself. Hanabi tries to obtain Hyōka's permission for this, but the conversation ends in a fight. Without her sister's approval, Hyōkei decides to go through with the transformation regardless. The process of becoming human requires Hanabi's blood, which Hanabi offers. Hyōkei then becomes human and leaves her sister. This event becomes the breaking point that permanently damages the relationship between Hanabi and Hyōka.

The setting is the same world as the main series Ore no Kanojo ni Nanika Yōkai, where humans and youkai coexist. The story is told in a four-panel format. The main characters are Hanabi Fukuzumi, a human girl who reacts badly to youkai, and Hyōka Shiroishi, a powerful snow youkai who is the future leader of the northern youkai and who has difficulty forming connections due to her cold personality and her position. Both are seventeen years old. Other important characters include Akira, Hanabi's childhood friend; Tōji, Hyōka's fiancé; and Hyōkei, Hyōka's younger sister who longs to become human. The narrative arc centers on the formation and eventual dissolution of the friendship between Hanabi and Hyōka, as well as a mysterious presence that affects the present-day events of the main series.