Despite the fact that morbidity and mortality rates due to dengue infection in Indonesia are relatively high, a dengue vaccination has not yet been introduced. Next to vaccination, Wolbachia-infected mosquitoes and health education have been considered to be potential interventions to prevent dengue infection in Indonesia. This study was aimed to analyse the cost-effectiveness of dengue vaccination in Indonesia whilst taking Wolbachia and health education programs into account. An age-structured decision tree model was developed to assess the cost-effectiveness. Approximately 4,701,100 children were followed-up in a 10-year time horizon within a 1-year analytical cycle. We compared three vaccination strategies: one focussing on vaccination only, another combining vaccination and a Wolbachia program, and a third scenario combining vaccination and health education. All scenarios were compared with a no-intervention strategy. The result showed that only vaccination would reduce dengue fever (DF), dengue haemorrhagic fever (DHF), and dengue shock syndrome (DSS) by 123,203; 97,140 and 283 cases, respectively. It would save treatment cost at $10.3 million and $6.2 million from the healthcare and payer perspectives, respectively. The combination of vaccination and a Wolbachia program would reduce DF, DHF and DSS by 292,488; 230,541; and 672 cases, respectively. It would also save treatment cost at $24.3 million and $14.6 million from the healthcare and payer perspectives, respectively. The combination of vaccination and health education would reduce DF, DHF, and DSS by 187,986; 148,220; and 432 cases, respectively. It would save treatment cost at $15.6 million and $9.4 million from the healthcare and payer perspectives, respectively. The incremental cost-effectiveness ratios (ICERs) from the healthcare perspective were estimated to be $9995, $4460, and $6399 per quality-adjusted life year (QALY) gained for the respective scenarios. ICERs from the payer perspective were slightly higher. It can be concluded that vaccination combined with a Wolbachia program was confirmed to be the most cost-effective intervention. Dengue infection rate, vaccine efficacy, cost of Wolbachia program, underreporting factor for hospitalization, vaccine price and mortality rate were considered to be the most influential parameters affecting the ICERs.