This is a case of a young male patient with no known prior risk factors who presented for acute-onset right-sided neurological deficits suspicious for stroke, and magnetic resonance angiography (MRA) identified the development of an occlusion at the level of a basilar artery (BA) fenestration in the setting of right vertebral artery occlusion. The patient was treated with dual-antiplatelet therapy in the hospital and was able to return to work shortly after discharge. The case provides insights into several possibilities for the clinical significance of BA fenestration and its potential causal or contributory relationship with ischaemic stroke of the brainstem.