A new cyprinid fish, Nipponocypris takayamai sp. nov. is described from the Middle Pleistocene Nogami Formation in Oita Prefecture, Northern Kyushu, Japan. Nipponocypris takayamai differs from its congeners in the following combination of characters: the sensory canal of the parietal not reach to the medial edge of the parietal, and its length longer than half the width of the parietal; the notch of the orbital margin of the frontal weak; the dorsal margin of opercle concave; the posterodorsal margin of the fourth infraorbital L-shaped; the sensory canal of the dentary running slightly ventrally; 42–44 vertebrae; the flanges of the neural spines of the second and third preuralcentra elongated to the dorsal ends of the neural spines; eight supraneurals between the dorsal fin and the supraneural 3 bone; the dorsal fin base located slightly more posterior than the pelvic fin base; first three dorsal fin rays unbranched and unsegmented; eight dorsal fin rays, ten dorsal fin pterygiophores; and eleven anal fin pterygiophores with thirteen anal fin rays. A cladistic analysis suggests that this new species is related to N. sieboldii, N. koreanus and N. temminckii, and is probably the sister taxon to N. temminckii. This new species shows that an extinct species closely related to Recent Nipponocypris existed until the Middle Pleistocene in East Asia.