Vertebral artery fenestration is accidentally detected during angiography or autopsy. Spontaneous deep nuclear hemorrhage in association with vertebral artery fenestration is a very unusual finding in angiography. Such an unusual finding has not been reported in the English literature. Here, we report two cases of spontaneous deep nuclear hemorrhage that presented with features of raised intracranial pressure. Computed tomography revealed a deep nuclear acute bleed in both cases. Digital subtraction angiographic findings were normal other than the presence of a long segment vertebral artery fenestration. Both extracranial and intracranial variations were detected. Although the existence of vascular fenestration in the vertebrobasilar system produces less clinical importance, it may influence the management of cervical and intracranial pathologies to avoid iatrogenic injury.