Japanese encephalitis (JE) is an important viral encephalitis that is epidemic in Asia and is caused by Japanese encephalitis virus (JEV), a member of the genus Flavivirus. JEV was divided into five genotypes. Genotype 5 (G5) is, however, relatively neglected due to the limited number of cases and strains isolated. The first strain of G5 JEV (Muar strain) was isolated in Singapore in 1952 from a patient who came from Muar, Malaysia. The second strain (XZ0934) was isolated 57 years later in China indicating the re-emergence of the G5 JEV. A female patient who had been vaccinated against JE infected G5 JEV in Korea in 2015. JE is a vaccine-preventable disease and its incidence decreased as the use of vaccine increased in many Asian countries. G3 JEV was the main candidate for the current JE vaccines, which include attenuated, inactivated, and chimeric type vaccines. However, the vaccines available do not provide adequate levels of protection against G5 JEV, “old” genotype. Therefore, as a new threat, more research on this genotype is vital for the development of better detection methods, expanding surveillance to determine the possible chains of virus transmission, and developing a polyvalent JEV vaccine.