Oreki Houtarou is a minimalistic high school boy. One day, he joins the Classic Literature Club at his elder sister's request.

There he meets Chitanda Eru, Fukube Satoshi, and Ibara Mayaka. Chitanda is a calm beautiful girl but she turns into an embodiment of curiosity once she says, "I'm interested in it (Watashi, Kininarimasu)." Fukube is a smiling boy with a fantastic memory who calls himself a database. Ibara is a short girl and is strict with others and herself. She loves Fukube, but he always dodges her approaches.

They begin to investigate a case that occurred 45 years ago. Hints of the mystery are buried in an old collection of works of the former members of Classics Club. The collection is titled "Hyouka."