Background Vertebrobasilar junction fenestration is considered to be a subtype of fenestration of the proximal basilar artery, which has been described only in autopsy cases. The fenestration associated with a dissecting vertebral aneurysm is extremely rare. Case Description A 47-year-old man presented with subarachnoid hemorrhage. The four-vessel angiogram showed a fusiform dilatation with an intimal flap of the left vertebral artery distal to the origin of the posterior inferior cerebellar artery and a fenestration at the vertebrobasilar junction, in which a small limb of the fenestration arising from the distal portion of the left vertebral artery bridged the proximal basilar trunk, while another limb had a large diameter showing the same diameter as the basilar artery. The dissecting aneurysm was treated with body clipping by directly clipping the ruptured portion of the aneurysm via a suboccipital approach in an early operation 48 hours after the ictus. The patient had a good recovery and returned to his work. He is well at a 5-year follow-up. Conclusions The relevant angiographic features of the vertebrobasilar junction fenestration and the surgical treatment of such associated aneurysms are discussed.