Japanese encephalitis is an important cause of viral encephalitis in East and South Asia. Here we report the case of a 16-month-old boypresenting with a 7-day history of cough and runny nose, accompanied by fever. On clinical presentation, he developed repetitive general spasms and unconsciousness. A 4-fold increase was detected in serum immunoglobulin M antibody titers for Japanese encephalitis virus. Diagnosis of Japanese encephalitis was confirmed on the basis of several factors: seasonality, location, work or travel within endemic areas, mosquito bites, vaccination history, clinical features, serology, and brain magnetic resonance imaging (MRI). These findings suggest that when a patient with suspected Japanese encephalitis develops fever, headache, and a change in consciousness, typical hypothalamic lesions identified on brain MRI can clarify the diagnosis. Currently, Japanese encephalitis vaccination is the most direct and effective method of preventing this disease.