A new periotic of Numataphocoena yamashitai from the upper part of the Horokaoshirarika Formation (lower Pliocene), Numata, Hokkaido, Japan shows younger ontogenetic features in comparison to the matured holotype (NFL 7). The referred specimen of N. yamashitai is smaller (approximately 90% in size) than the physically and sexually matured holotype periotic. The holotype (NFL 7) and referred specimen (NFL 2617) show several differences owing to ontogenetic changes, such as: the holotype (NFL 7) has a more strongly swollen medial part of the anterior process, blunt anterior keel, rounded anterodorsal angle, deeper and clearer anterior incisure, more rounded pars cochlearis, deeper and narrower hiatus epitympanicus rather than a flat area, longer posterior process with an extra edge posterolaterally. N. yamashitai differs from other fossil phocoenids in having a narrower and sharper anterior part of the internal acoustic meatus and a robust anterior process. Haborophocoena toyoshimai similarly has a relatively narrow internal acoustic meatus and a robust anterior process, compared with other fossil phocoenids. Between N. yamashitai and H. toyoshimai, N. yamashitai has a narrower internal acoustic meatus and a more robust anterior process. These similarities imply a close relationship between Numataphocoena and Haborophocoena. The new specimen provides diagnostic features and insight into ontogenetic variation of N. yamashitai.