The Thai government implemented COVID-19 booster vaccines to prevent morbidity and mortality during the spreading of the Omicron variant. However, little is known about which types of vaccine should be invested in as the booster dose for the Thai population. This study aims to investigate the most cost-effective COVID-19 vaccine for a booster shot as empirical evidence for Thai policymakers. This study applied a stochastic simulation based on a compartmental susceptible-exposed-infectious-recovered model and included system dynamics in the model. We evaluated three scenarios: (1) No booster, (2) A viral vector vaccine as the booster dose, (3) An mRNA vaccine as the booster dose. The incremental cost-effectiveness ratio (ICER) was calculated based on provider perspectives. We found the number of cases in scenarios with viral vector and mRNA booster doses to be lower than in the non-booster group. Likewise, the number of deaths in the viral vector and the mRNA booster scenarios was threefold lower than in the no-booster scenario. Moreover, the estimated grand cost for the no-booster scenario was over 100 billion baht, while viral vector and mRNA scenario costs were 70 and 64.7 billion baht, respectively. ICER shows that viral vector and mRNA scenarios are more cost-effective than the no-booster scenario. Viral vector booster shot appeared to be slightly more cost-effective than mRNA booster shot in terms of death aversion. However, being boosted by an mRNA vaccine seemed slightly more cost-effective than a viral vector vaccine concerning case aversion. In conclusion, policies to promote COVID-19 booster shots in the Thai population by either mRNA or viral vector vaccines are likely to be worthwhile for both economic and public health reasons.