Japanese-B virus encephalitis (JE), the most common human endemic and epidemic encephalitis, usually has a uniphasic illness with a variable outcome. A 49-year-old woman with cognitive dysfunction from JE had improved over 3 weeks. Brain MRI revealed multiple lesions in the bilateral thalamus, caudate nuclei and medial temporal lobe. Two weeks after discharge, the patient showed re-aggravation of the cognitive dysfunction and lapsed into coma. We report a patient with JE having showed biphasic illness pattern.