We present a case of a 55-year-old woman with pontine infarction and fenestration of the basilar artery that was demonstrated using virtual endoscopy. The patient had motor weakness of the right side with sudden onset. Diffusion- and T2-weighted MR images revealed high signal intensities in the left pontine regions, and an MR angiographic examination showed the double-lumen sign of the basilar artery. An extensive duplication-type, nonseparated fenestration of the basilar artery was diagnosed by virtual endoscopy and craniocaudal communications with discrete openings were observed. We report a case of a patient with basilar artery fenestration and associated brainstem infarction.