In South Korea, the National Immunization Program offers a 23-valent pneumococcal polysaccharide vaccine (PPSV23) for the elderly; however, the 13-valent pneumococcal conjugate vaccine (PCV13) is not included, and vaccination is not offered to younger, at-risk populations. This study offers a comparative analysis of PCV13 and PPSV23 in Korea's adults, stratified by age and risk group. A Markov model with a lifetime horizon was developed from the healthcare perspective. Data sources included the Health Insurance Review & Assessment Service, Korea Centre for Disease Control & Prevention and Korean medical institutions. An expert panel tested data validity. The CAPiTA trial and Cochrane meta-analysis were used to obtain vaccine effectiveness data. Regardless of co-morbidity, when the sequential PCV13-PPSV23 strategy was compared to that using PPSV23-only, in elderly populations, the incremental cost-effectiveness ratio (ICER) was 3,300 USD per quality-adjusted life years (QALY). For the risk group aged ≥65 years, the ICER of the addition of PCV13 over the existing PPSV23-only strategy was 3,404 USD/QALY. However, on replacing PPSV23 with PCV13, for all elderly populations, an ICER of 1,421 USD/QALY resulted; for the risk group aged ≥65 years, the ICER was 1,736 USD/QALY. For the 18-64 year-old risk group, the sequential PCV13-PPSV23 strategy yielded an ICER of 3,629 USD/QALY over the PPSV23-only strategy, and 6,643 USD/QALY compared to no vaccination. Thus, the PCV13→PPSV23 combination strategy for elderly populations was found to be a cost-effective alternative to the current National Immunization Program regardless of co-morbidity. This finding was the same as that for younger, at-risk populations.