We report a case of atlantoaxial subluxation with bilateral high-riding vertebral artery with narrow isthmus. Because of the potential risk of bilateral vertebral artery injury, we performed atlantoaxial fixation using rod and screw instead of transarticular screw fixation. Although postoperative computed tomography reconstruction demonstrated slight breach of bilateral vertebral artery groove, postoperative angiography showed no evidence of vertebral artery injury. Though technically demanding, atlantoaxial fixation using rod and screw can be a one of the treatment options for atlantoaxial instability with bilateral high riding vertebral artery.