A 53-year-old male presented with repeated vertebrobasilar insufficiency on turning the head to the left. Angiography revealed severe stenosis of the dominant right vertebral artery at the atlantoaxial level in this position. Decompression surgery for the affected vertebral artery at the transverse foramen of the atlas was planned. However, surgery revealed an aberrant course of the artery, turning at the orifice of the transverse foramen of the atlas and perforating the dura at the occipitoatlantal level after passing through the bony canal of the atlas. Therefore, decompression was performed at the bony canal, which was the contributing site, and the symptoms improved. Bow hunter's stroke may be caused by atlantoaxial arterial anomalies, so accurate preoperative evaluation of the region is necessary to avoid anatomical confusion at surgery.