This paper presents the case report of an 11-year-old boy with an acute dissection with thrombosis of the left vertebral artery and thrombosis of the basilar artery. The patient was treated with acute systemic thrombolysis, followed by intra-arterial thrombolysis, without any clinical improvement, showing left hemiplegia, bilateral clonus, hyperreflexia, and impaired consciousness. MRI indicated persistent thrombosis of the arteria basilaris with edema and ischemia of the right brainstem. Heparinization for 72 hours, followed by a two-week LMWH treatment and subsequent oral warfarin therapy, resulted in a lasting improvement of the symptoms. Vertebral artery dissection after minor trauma is rare in children. While acute basilar artery occlusion as a complication is even more infrequent, it is potentially fatal, which means that prompt diagnosis and treatment are imperative. The lack of class I recommendation guidelines for children regarding treatment of vertebral artery dissection and basilar artery occlusion means that initial and follow-up management both require a multidisciplinary approach to coordinate emergency, critical care, interventional radiology, and child neurology services.