A case of persistent primitive proatlantal intersegmental artery (PPPIA) associated with a ruptured basilar bifurcation aneurysm was reported. A 44-year-old male with sudden headache was admitted to our hospital. CT scan revealed subarachnoid hemorrhage. Cerebral angiography revealed anomalous anastomosis between the internal carotid artery and the vertebral artery at the proatlantal region. This anastomosis branched off from the left internal carotid artery at the C4 level and joined the horizontal portion of the left vertebral artery. It was thought to be PPPIA. Angiography also revealed an aneurysm of the basilar bifurcation which was responsible for the patient's subarachnoid hemorrhage. The aneurysm was successfully treated by endovascular embolization with Guglielmi detachable coils in an acute stage, and resulted in good outcome. PPPIA with basilar bifurcation aneurysm has not been presented or reported in the literature to date. To our knowledge, this is the first report of such an association of vascular anomalies. The frequency of PPPIA combined with the intracranial aneurysm is relatively high, whereas the occurrence of PPPIA is extremely rare. Therefore, it was suggested that some congenital and/or hemodynamic factors changed by PPPIA may affect the pathogenesis of intracranial aneurysms.