A new fossil species of the genus Ceratophyus Fischer von Waldheim, 1824, was discovered in the Shiobara Group (Chibanian, ca. 0.3 Ma) of the Middle Pleistocene distributed in Nasushiobara City, Tochigi Prefecture, Japan. This fossil is female, large in size (ca. 25 mm), well preserved, and nearly completely preserved. The genus Ceratophyus is not distributed in modern Japan. This is the first discovery of a fossil of the genus Ceratophyus and the first report of a certain extinct species from the Shiobara Group. The genus Ceratophyus is now fragmentarily distributed in the Holarctic region of the world, but the discovery of the fossil suggests that the genus was widely distributed throughout the world during the Middle Pleistocene. Notably, the fossil was discovered by a student during a high school lesson from a rock brought into the classroom. We consider the examined fossil to be morphologically different from all known extant species of the genus, and therefore we describe it as Ceratophyus yatagaii sp. nov.