The late Palaeogene represents a crucial time in cetacean evolution that witnessed the origin of modern baleen and toothed whales (Neoceti) from their “archaeocete” ancestors. So far, this fundamental transition has been discussed mainly in terms of cranial morphology, whereas descriptions of postcranial material remain rare. Here, we report a small cetacean humerus from the Nichinan Group (lower Oligocene to lower Miocene), Kushima City, Miyazaki Prefecture, southern Kyushu, Japan. Our specimen resembles archaeocete humeri in being proximodistally elongate and in retaining a distinct deltoid ridge, but shares with neocetes the defining feature of an immobilised elbow joint. It resembles most Oligocene odontocetes in its small size and in lacking a notch marking the position of the distal epiphysis, and is furthermore similar to the enigmatic Microzeuglodon in having a transversely compressed shaft. A morphometric analysis based on five linear measurements, however, fails to cluster our specimen with any other known group of cetaceans, indicating that it is not easily referable to either basal mysticetes or odontocetes. Therefore, we here classify it as Neoceti incertae sedis.