Risk of injury to normal vertebral artery (VA) unlike that associated with an anomalous VA is infrequent during posterior C1–C2 reduction for congenital atlantoaxial dislocation (AAD). An ischemic event resulting from such indirect injury is a rare occurrence. A 14-year-old boy with severe AAD/basilar invagination underwent C1–C2 joint manipulation and fixation with an uneventful intraoperative course. Although his immediate postsurgical period was unremarkable, he sustained sudden and rapid neurological worsening on day 3. He developed multiple posterior fossa infarcts and finally succumbed. VA can be indirectly injured possibly due to excessive distraction/manipulation of C1–C2 joints. The lesson learnt is that anticipation of such injuries along with proactive anticoagulation treatment can potentially alter patient outcome.