This study investigates the change of endothelial cell morphology and function at the rabbit basilar bifurcations in response to sustained high blood flow after bilateral common carotid artery ligation. Fifteen adult female New Zealand white rabbits were divided into experimental and sham control groups. The experimental group was subjected to bilateral common carotid artery ligation to increase the compensatory basilar artery flow. Basilar artery flow was monitored by transcranial Doppler after surgery. The endothelial cells at the arterial bifurcations were studied morphologically by electron microscopy and immunohistochemistry using β-catenin antibodies. Basilar artery flow increased significantly following common carotid artery ligation. Early-stage basilar artery bifurcation aneurysms were present in all rabbits at three months after ligation. The endothelial cells changed from a fusiform to column shape at the basilar artery bifurcation. Gaps between endothelial cells of the experimental group appeared wider in the electron microscopic photographs compared with those of the control group. The expression of endothelial β-catenin at the arterial bifurcations also decreased. This study is the first to present endothelial cell changes of basilar artery bifurcation in response to sustained high blood flow in rabbits. Endothelial cell impairment possibly initiates aneurysm formation.