The persistent transmission of Japanese encephalitis virus (JEV) in Taiwan necessitates exploring the risk factors of occurrence of Japanese encephalitis (JE). The purpose of this study was to assess the relationship between meteorological factors and the incidence of JE in Taiwan. We collected data for cases of JE reported to the Taiwan Centers for Disease Control (Taiwan CDC) from 2000 to 2014. Meteorological data were obtained from the Taiwan Central Weather Bureau.