Japanese encephalitis (JE), once a major public health problem in South Korea, has declined since the 1980s, as a result of improved living conditions, a mosquito eradication program, and a national JE vaccination program, which includes annual booster vaccine for all children less than or equal to 15 years of age. Increased immunity has greatly reduced illness and death; however, vaccine adverse effects are increasing, and a National Compensation Program for Vaccine Injury was begun in 1995. This article reviews past successes, current problems, and future direction of the JE vaccination program in South Korea.