BACKGROUND: Currently in Japan, both 23-valent pneumococcal polysaccharide vaccine (PPSV-23) and 13-valent pneumococcal conjugate vaccine (PCV-13) are available for the elderly for the prevention of S. pneumoniae-related diseases. PPSV-23 was approved in 1988, while the extended use of PCV-13 was approved for adults aged 65 and older in June 2014. Despite these two vaccines being available, the recently launched national immunisation programme for the elderly only subsidised PPSV-23. The framework of the current immunisation programme lasts for five years. The elderly population eligible for the subsidised PPSV-23 shot for the 1st year are those aged 65, 70, 75, 80, 85, 90, 95 and ≥ 100. While from the 2nd year to the 5th year, those who will age 65, 70, 75, 80, 85, 90, 95 and 100 will receive the same subsidised shot. METHODS: We performed economic evaluations to (1) evaluate the efficiency of alternative strategies of PPSV-23 single-dose immunisation programme, and (2) investigate the efficiency of PCV-13 inclusion in the list for single-dose pneumococcal vaccine immunisation programme. Three alternative strategies were created in this study, namely: (1) current PPSV-23 strategy, (2) 65 to 80 (as "65-80 PPSV-23 strategy"), and (3) 65 and older (as "≥ 65 PPSV-23 strategy"). We constructed a Markov model depicting the S. pneumoniae-related disease course pathways. The transition probabilities, utility weights to estimate quality adjusted life year (QALY) and disease treatment costs were either calculated or cited from literature. Cost of per shot of vaccine was ¥ 8,116 (US$74; US$1 = ¥ 110) for PPSV-23 and ¥ 10,776 (US$98) for PCV-13. The model runs for 15 years with one year cycle after immunisation. Discounting was at 3%. RESULTS: Compared to current PPSV-23 strategy, 65-80 PPSV-23 strategy cost less but gained less, while the incremental cost-effectiveness ratios (ICERs) of ≥ 65 PPSV-23 strategy was ¥ 5,025,000 (US$45,682) per QALY gained. PCV-13 inclusion into the list for single-dose subsidy has an ICER of ¥ 377,000 (US$3,427) per QALY gained regardless of the PCV-13 diffusion level. These ICERs were found to be cost-effective since they are lower than the suggested criterion by WHO of three times GDP (¥ 11,000,000 or US$113,636 per QALY gained), which is the benchmark used in judging the cost-effectiveness of an immunisation programmne. CONCLUSIONS: The results suggest that switching current PPSV-23 strategy to ≥ 65 PPSV-23 strategy or including PCV-13 into the list for single-dose subsidy to the elderly in Japan has value for money.