OBJECTIVES: This study aims to assess the cost-effectiveness of hepatitis A vaccination in Indonesia, including an explicit comparison between one-dose and two-dose vaccines. METHODS: An age-structured cohort model based on a decision tree was developed for the 2012 Indonesia birth cohort. Using the model, we made a comparison on the use of two-dose and one-dose vaccines. The model involves a 70-year time horizon with 1-month cycles for children less than 2 years old and annually thereafter. Monte Carlo simulations were used to examine the economic acceptability and affordability of the hepatitis A vaccination. RESULTS: With the vaccine price of US$ 4.49 per dose, the implementation of the hepatitis A vaccine from the societal perspective would yield incremental-cost-effectiveness-ratios (ICERs) at US$ 9,194 and US$ 4,577 for the two-dose and one-dose vaccine schedules, respectively. Considering the 2012 gross-domestic-product (GDP) per capita in Indonesia of US$ 3,557, the results indicate that hepatitis A vaccination would be a cost-effective intervention, both for the two-dose and one-dose vaccine schedules. Vaccination would be 100% affordable at budgets of US$ 89,918,000 and US$ 46,778,000 for the implementation of the two-dose and one-dose vaccine schedules, respectively. CONCLUSIONS: The implementation of hepatitis A vaccination in Indonesia would be a cost-effective health intervention under the market vaccine prices.  Given the budget limitations, the use of a one-dose-vaccine schedule would be more realistic to be applied than a two-dose schedule. The discount rate, vaccine price, vaccine efficacy and mortality rate were the most influential parameters impacting the ICERs.