A comparative study of MRI and pathology was performed on a case of cryptococcal meningoencephalitis. An 11-year-old female presented with confusion and vomiting. On admission, CSF examination revealed spherical fungal cells with mild pleocytosis, decreased glucose and elevated protein level. MRI showed multiple punctate lesions in the basal ganglia with high intensity on T2-weighted image, while enhanced MRI revealed diffuse meningeal involvement. Post-mortem examination disclosed that the T2-weighted lesions found in the basal ganglia were aggregated small cystic lesions consisting of a cryptococcal invasion of Virchow-Robin spaces, termed "soap bubble lesions", characteristic findings of cryptococcal meningoencephalitis. Thus MRI findings of the basal ganglia and meninges may help to diagnose cryptococcal meningoencephalitis.