OBJECTIVES: Vaccination would lead to reduce the incidence and mortality of an infectious disease and then increase the years of life and productivity for entire society. But, determination of vaccination coverage rate is usually not taken its economic burden into account. This study aims to use a transmission dynamic model (TDM) based on a susceptible-infectious-recovered (SIR) model, a system of differential equations, to find optimal vaccination coverage rate based on the economic burden of an infectious disease. METHODS: Vaccination for pneumococcus diseases was used as an example to demonstrate the main purpose. 23-valent pneumococcal polysaccharide vaccines (PPV23) and13-valent pneumococcal conjugate vaccines (PCV13) have been shown their cost-effectiveness in elderly and children, respectively. Scenarios analysis of PPV23 to the elderly aged 65+ years and PCV13 to children 5 years and under was applied to assess the optimal vaccination coverage rate based on the economic burden. All epidemiological parameters were derived from the Taiwan’s National Health Insurance Research Database, all cost parameter were derived from the Taiwan’s Ministry of the Interior and the vaccine efficacy was obtained from the literatures. Various vaccination coverage rate, the vaccine efficacy and all epidemiological parameters were all substituted into to TDM and all differential equations were solved using the fourth-order Runge–Kutta method implemented in R Statistical Software. RESULTS: If the he coverage rate of PPV23 for the elderly and PCV23 for the children both reach to 50%, the economic burden due to pneumococcus disease will be minimized approximately. CONCLUSIONS: This study provided an alternative perspective from the economic burden of diseases to obtain a vaccination coverage rate using the TDM. This will provide valuable information for vaccination policy decision makers.