Polypterus is an African freshwater fish genus comprising 13 extant species and 3 fossil species, including †P. faraou, which is based on a single articulated specimen from the Late Miocene (~7 Ma) of Chad. Recently, †P. faraou has been suggested to be conspecific with P. bichir, as its meristic values fall within the expected range of variation for P. bichir, which entirely encompasses the diagnoses of both taxa. In this study, we use X-ray tomography and three-dimensional reconstructions to generate new data on the cranial anatomy of †P. faraou and compare it with P. bichir in order to test the validity of the fossil species. Owing to the fossil’s exceptional preservation, all cranial regions and the pectoral girdle were described, either fully or partially. Regarding meristic characters, we corroborate that †P. faraou indeed falls within the range expected for P. bichir. However, we were able to distinguish the two species based on features of the opercular region and posterior ceratohyal morphology. Accordingly, we propose an emended diagnosis for †P. faraou, characterized by a proportionally longer ventral process of the preopercle, a higher subopercle that extends well beyond the mid-height of the opercle, an opercle with a more triangular outline, and a rounded posterior ceratohyal. Although these species show few morphological differences, we present here the first cranial osteological diagnosis for this genus, highligthing its importance for advancing the understanding of cranial morphology in polypterids.