Vertebrobasilar junction fenestration is a rare congenital anomaly which is commonly seen with an aneurysm formation. Because of the complex anatomical structure of this area complicates the surgical intervention, endovascular coil treatment of aneurysm is an alternative method. Several fenestration-related aneurysms may not be detected by 2D conventional angiography imaging due to their considerably thin and short structure or small size. By 3D rotational digital subtraction angiography, small-sized fenestrations can be examined at the intended plane from various angles. This method enables us to plan the endovascular intervention in detail by revealing orientation, neck, origin of perforator arteries, and the relation between aneurysm and fenestration. In the present case, we present the angiographic results of the case with vertebrobasilar junction fenestration, along with endovascular treatment of the ruptured aneurysm.