Fibromuscular dysplasia (FMD) is a systemic arteriopathy which tends to affect renal arteries followed by cervicocranial vessels. It can lead to cerebral infarction if cephalic arteries are involved. FMD is an unusual cause of stroke in childhood that generally affects the carotid area. Only four cases of vertebral FMD and subsequent stroke have been reported previously and we present the youngest patient of all. A healthy 3-year-old female was admitted to Hospital Doce de Octubre in Madrid, Spain with cerebellar infarction. Angiography disclosed basilar artery thrombosis and typical signs of FMD in both vertebral arteries. No other angiographic alteration was noted in the other vessels studied. Her phenotype and other investigations were unremarkable. The patient was treated with anti-aggregation therapy (aspirin) and the outcome was excellent. Investigation of the occurrence in childhood of this kind of arteriopathy may lead to clarification of its natural history and speculation about its unclear pathogenesis.