The Japanese Encephalitis (JE) virus circulation in Indonesia was first documented in Lombok in 1960, and the virus was first isolated in 1972 from Culex tritaeniorhynchus in Bekasi, West Java and Kapuk, West Jakarta. Since then, Indonesia has been recognized as an endemic country for JE transmission. Up to now, JE cases have been found in at least 29 provinces, with Bali, West Kalimantan, East Nusa Tenggara, West Java and East Java, being the areas of highest incidence. However, routine surveillance on JE has not been established at the national level even though many surveys were conducted. JEV has been isolated from 10 mosquito species: Culex tritaeniorhynchus, Cx. gelidus, Cx. vishnui, Cx. fuscocephala, Cx. bitaeniorhynchus, Cx. quinquefasciatus, Anopheles vagus, An. kochi, An. annularis, and Armigeres subalbatus. Culex tritaeniorhynchus is the main JE vector in Indonesia. JE has been detected throughout the Indonesian archipelago from West to East. However, due to a lack of routine, systematic and standardized diagnostic approaches, the JE burden has still not been clearly established yet. Long term and systematic JE surveillance across Indonesia is a priority, the burden needs to be better assessed and appropriate control measures must be implemented.