Background: Fabry disease is very rare and often delayed in diagnosis. Described herein are Fabry disease causes angiitis of the central nervous system. MRI black blood sequence has a unique advantage in showing vascular wall. It can clearly show the angiitis. Case presentation: A 27-year-old man came to our hospital for treatment because of "diplopia 6d". The patient was eventually diagnosed with Fabry disease causes angiitis of the central nervous system by a series of examinations. Then，we treated patient with hormones and the symptoms relieved. Two months later，the initial vasculitis was gone，but the new vasculitis appeared. Four months later，the last lesion disappeared，but the new lesion appeared. Conclusions: This case prompts the clinician should use MRI black blood sequence scan in time when young patients have repeated strokes and the lesions are migratory. If vasculitis is found and other systemic lesions are combined，we should think of the possibility of Fabry disease.