BACKGROUND: Signs of brainstem ischemia in children may be subtle, and outcome following basilar artery occlusion is often poor. There currently are no guidelines in children regarding the best methods to diagnose and treat basilar artery occlusion. METHODS: Case report and literature review. RESULTS: We describe the presentation and management of recurrent basilar artery occlusion in a previously healthy 5-year-old boy with vertebral artery dissection. Treatment included emergent intra-arterial tPA and mechanical thrombolysis of basilar artery clot, followed by later coiling of the vertebral artery to prevent recurring episodes of basilar artery ischemia. CONCLUSION: Management of brainstem stroke in children requires coordination of neurology, critical care, and interventional radiology services. Delayed intra-arterial thrombolysis and vertebral artery coiling can be successfully used to treat basilar artery occlusion and prevent the recurrence of brainstem ischemia in children.