Using decision analysis, we estimated benefits, risks, and costs of implementing the Japanese encephalitis (JE) vaccination program in children aged 18 months and 6 years in Thailand.  The costs for inclusion of JE vaccine into the routine immunization program at 18 months and 6 years are $ 2.16 and $ 3.68 per person, respectively.  In the baseline model, the JE vaccination program will prevent 124 JE cases in the program for 18 months old children and 153 JE cases in the program for 6 years old children. The 18 month child program is more cost-effective than the 6 year child program. The cost-effectiveness ratio in the 18 month child program is $ 15,715 compared with $ 21,661 in the 6 year child program. The benefits of the JE vaccination program are the savings in treatment cost, disability care, and the future lifetime earnings from JE prevented.  The18 month child program will save $ 72,922 per one prevented JE compared with $ 66,197 in the 6 year child program. The JE vaccination program is cost-beneficial under the base-case assumption.  Sensitivity analysis which alters various assumptions indicates that the JE vaccination program is worth implementing unless the incidence of JE is less than 3 per 100,000 population. Otherwise, the cost of vaccination has to be reduced.