Japanese encephalitis virus (JEV) causes acute Japanese encephalitis (JE) in humans and reproductive disorders in pigs. There are approximately 68,000 cases of JE worldwide each year, with approximately 13,600 to 20,400 deaths. JE infections have a fatality rate of one-third, and half of the survivors experience permanent neurological sequelae. The disease is prevalent throughout the Asia–Pacific region and has the potential to spread globally. JEV poses a serious threat to human life and health, and vaccination is currently the only strategy for long-term sustainable protection against JEV infection. However, licensed JEV vaccines are not effective against all strains of JEV. To date, there are no drugs approved for clinical use, and the development of anti-JEV drugs is urgently needed. Natural products are characterized by a wide range of sources, unique structures and low prices, and this paper provides an overview of the research and development of anti-JEV bioactive natural products.