Most of the cranial sutures that outline individual bones of the skull are not visible in the holotype, and are often obscured by cracks. However, the overall shape of Prodiplocynodon is similar to that of basal alligatoroids. Many of the features seen in Prodiplocynodon are common among eusuchians. The skull is short and triangular, being around in length. The orbits, or eye sockets, are quite large and subtriangular. The teeth are short and somewhat sharp, and in comparison to modern crocodiles show little variation. The orbits face directly upwards, but this may have been the result of slight compression in the holotype skull. The external nasal aperture, the opening for the nostrils, is very large. There is a constriction at the point of contact between the premaxilla and maxilla which would have been an area of reception for a large mandibular tooth. In Prodiplocynodon, the constriction is not deep, being intermediate between that of Alligator and Crocodylus.
