The authors report a case of fatal stroke due to thrombosis of a cerebral arteriovenous malformation (AVM) in a young patient. The patient presented with a progressive severe headache that had lasted for a few days, followed by a rapid deterioration in the level of consciousness. Computed tomography and magnetic resonance imaging were immediately performed, and the images showed a large area of venous ischemia in the left hemisphere as well as a left temporal pial AVM. An emergency decompressive craniectomy was unsuccessful in preventing deterioration in the patient's condition. An autopsy examination revealed a thrombosed AVM leading to a wide area of venous ischemia and massive brain swelling. Thrombophilia investigations identified a heterozygous mutation at position 20209 of the prothrombin gene, a recently reported rare prothrombotic defect. Acute neurological decline after spontaneous thrombosis of an intracranial AVM is rare, and an association with the prothrombin defect in this patient is likely.