A 69-year-old female presented with trigeminal neuralgia caused by tortuous vertebrobasilar artery associated with primitive trigeminal artery (PTA) and agenesis of the ipsilateral internal carotid artery (ICA). Left vertebral angiography showed marked elongation of the left vertebral artery and filling of the left ICA via the PTA. Bone window computed tomography suggested agenesis of the left ICA. Intraoperative findings showed that the vertebrobasilar junction had compressed the root entry zone of the trigeminal nerve. The neuralgia improved immediately after microvascular decompression. There has been no recurrence for 20 months. Trigeminal neuralgia may be caused by a tortuous vertebrobasilar system due to hemodynamic stress associated with PTA and agenesis of the ICA.