Japanese encephalitis (JE) is one of the emerging infectious diseases now widespread in Asia, with recent extension into Torres Strait in northern Australia. In Indonesia, JE was not considered to be a serious clinical problem, although seroprevalence studies showed high prevalence of JE-neutralizing antibody in residents of Java, Kalimantan, Bali, with low prevalence in Sulawesi, Maluka and Irian Jaya. Confirmed clinical cases of JE have been rare in Indonesia and mainly have been reported in the west, and in tourists visiting Bali. No clinical cases of JE have been reported from Irian Jaya. This paper describes a clinical case of JE in a child from Irian Jaya and its confirmation by serology.