A new specimen of the Early Pliocene porpoise Haborophocoena toyoshimai, comprising an incomplete cranium, was discovered from the Embetsu Formation near the locality of H. minutus, Haboro Town, Hokkaido, Japan. The specimen is a juvenile skull of H. toyoshimai, comparable in size to the congeneric H. minutus. It confirms and/or adds some characters that define H. toyoshimai. It is now clear that the structure of the posterior part of the palate is unique to H. toyoshimai among phocoenids. It is markedly deep dorsoventrally at the level of the midlength of the orbit. In ventral view, the palatal face of the pterygo-palatine complex is distinct in having a sharp and sinuous lateral edge. The palatal surface of the pterygo-palatine complex is gently concave. A prenarial triangle anteromedial to the premaxillary eminence is depressed. The new specimen also reveals possible ontogenetic variation.