We describe an asymmetrical basal delphinoid skull from the upper lower Miocene Yamato Formation of Hokkaido, northern Japan. The skull shows clear cranial asymmetry: the nasal process of the left premaxilla is longer than that of the right one; the mesethmoid and frontals are left skewed 2.9°; and the right nasal is larger than the left one. Evaluation of the deformation of the fossil based on the carbonate content of the matrix indicates that the concretion in which the skull was found formed in an early stage of diagenesis and that the present specimen was not affected by compaction during diagenesis. A cladistic analysis including the new specimen shows cranial asymmetry among Delphinoidea extends back to the late early Miocene in the fossil record, and supports the hypothesis that cranial asymmetry in basal delphinoids is more common than previously thought. On the other hand, trait analyses suggest that the common ancestor of Delphinoidea had a symmetrical skull. We hypothesize that some extinct odontocetes that had symmetrical crania were able to produce narrow-band high-frequency clicks to avoid predation, as in extant symmetrical cranial species.