Background: Fabry disease is rare, and the diagnosis is often delayed. Here, we describe a case of Fabry disease resulting in vasculopathy of the central nervous system. Magnetic resonance (MR) black-blood sequence (three-dimensional T1 volumetric isotropic turbo spin echo acquisition), with the unique advantage of imaging the vascular wall, facilitated a clear identification of the vasculopathy. Case presentation: A 27-year-old man visited our hospital for the treatment of " double vision 6d." After a series of examinations, the patient was diagnosed with Fabry disease, which caused vasculopathy of the central nervous system. Subsequently, the patient was treated with corticosteroids and his symptoms were attenuated. Two months after the initial treatment, the initial lesion in the vascular vessel disappeared, however, a new lesion appeared. Similarly, four months after the initial treatment, although the previous lesion disappeared, a new lesion appeared. Conclusions: This case highlights that clinicians should use MR black-blood sequence scan in a timely manner in case of young patients with migratory lesions of brain. In case of detection of a vascular lesion in combination with other systemic lesions, the possibility of Fabry disease should be considered.