This report describes two patients with fenestrated basilar artery aneurysms, and one of the patients underwent a postmortem examination. In our cases, the aneurysms arose at the proximal end of the fenestration, which involved the proximal third of the basilar artery. Subtraction angiography and oblique projections were essential in diagnosing the aneurysms. Complete neck clipping was successfully performed through a lateral suboccipital approach in the two cases. Technical aspects of neck clipping of the aneurysm of this unique location are discussed. Pathogenesis of these rare aneurysms is also discussed with clinical and histopathological data.