A new fossil odontocete genus and species, Numataphocoena yamashitai is from the Early Pliocene Horokaoshirarika Formation, Numata, central Hokkaido, Japan. The porpoise was probably buried in relatively shallow marine sediments. This specimen consists of an incomplete skull, a right periotic and tympanic bulla, a posterior part of the right mandible, 23 isolated teeth, a nearly complete vertebral column, a chevron, incomplete right and well-preserved left scapulae, a right forelimb including humerus, radius, ulna, and a few indetermined carpals, and several ribs, all the same individual. The ankylosis of the epiphyses to vertebral bodies and to long bones, such as humerus, radius and ulna, shows that this individual reached both sexual and physical maturity; the animal in life was probably about 220 cm long. The cranial vertex has an elevated frontal knob, and the tooth crown is spatulated; both are characteristic of phocoenids. Numataphocoena yamashitai shows many primitive features such as premaxillae with less atrophied posterior extremities extending far posteriorly almost to hinder margin of the narial fossa, robust zygomatic processes, a periotic with massive anterior process and rugose posterior process, humerus long relative to radius or ulna, and free cervical vertebrae. The axial skeleton is significantly different from that of extant relatives in its a small number of vertebrae with anteroposteriorly broad transverse processes, and a long humerus relative to the radius and ulna.