Persistent primitive hypoglossal artery (PPHA) is a rare embryonic carotid-vertebrobasilar artery anastomosis, which has been often found accidentally. The PPHA is a unique anastomosis, among all the embryonic persistent fetal anastomosis, to act as a sole supply to the vertebrobasilar circulations. Here, we experienced a case of thrombotic cerebral infarction caused by atherosclerotic internal carotid artery (ICA) stenosis from which a concurrent PPHA arise. The case involved a 79-year-old male who had suffered from thrombotic strokes twice within a half year. Since the oral medication of anti-platelets drug failed to prevent stroke events, the ICA lesion was treated by carotid artery stenting (CAS). There have been several publications with respect to the surgical treatment for the ICA stenosis coinciding with a PPHA, where especially concerns for the inherent risks to damage the whole central nervous system were debated. After careful consideration and planning, CAS using a distal filter protection was successfully performed without complications. We report the details of the case along with literature reviews.