OBJECTIVES: According to World Health Organization, pneumococcal related diseases is a major public health concern in the world, especially for those under 2 years of age and older adults. The objective of this analysis is to evaluate the cost effectiveness of vaccinating the Brazilian population  65 years of age and older with the 13-valent pneumococcal conjugate vaccine (PCV 13) in comparison to the 23-valent pneumococcal polysaccharide vaccine (PPV 23), each as a single dose, from the public payer perspective. METHODS: In order to estimate the costs and the impact of the pneumococcal disease over a 35-year time horizon period, including invasive pneumococcal disease, hospitalized pneumonia and non complicated pneumonia, a patient level microsimulation model simulating vaccination and outcomes of one cohort of 12,653,613 individuals over 65 years of age was adapted to the Brazilian public health care system. The probabilities and direct medical costs were extracted from literature review and DATASUS for January 2011, with costs presented in US$ 2010. The effectiveness measures were expressed as cases of pneumococcal diseases avoided,  overall deaths avoided, and life years (LYs) saved. Probabilistic sensitivity analyses were conducted considering key variables.  A discount rate of 5% was applied. RESULTS: Vaccinating with PCV13 prevents 349 additional cases of acute meningitis, 1,589 cases of invasive pneumococcal disease, 100,158 hospitalized pneumonia, 12,954 non complicated pneumonia and 30,904 deaths, saving 139,189,74 LYs compared to PPV23 over 35 years. The total costs including vaccination costs and medical costs resulted in US$135,625,000 less for PCV13 compared to PCV23 (US$5,875,625,000 vs. US$5,740,000,000). The model showed robustness through sensitivity analyses. CONCLUSIONS: The analysis suggests that vaccinating adults with PCV13 in Brazil is cost-saving compared to PPV23. The results in economic and disease burden are substantial and they support the decision making in favor of PCV13 for its high impact in public health.