We observed a rare case of the right persistent hypoglossal artery (PHA) in the posterior cranial fossa of a deceased 74-year-old Japanese man who did not have any clinical manifestations related to this anomaly when alive. The large-sized PHA originating from the cervical internal carotid artery passed through the hypoglossal canal together with the hypoglossal nerve and reached the posterior cranial fossa to anastomose the basilar artery. In addition, the ipsilateral vertebral artery and bilateral posterior communicating arteries were hypoplastic. Here, we discuss the developmental mechanisms underlying the formation of the PHA and the spectrum of diseases related to its presence.