Low vaccination rates with pneumococcal vaccine in elderly persons in Japan are thought to be related to low levels of public subsidy. We previously reported that larger subsidies were significantly associated with elevated vaccination rates with the 23-valent pneumococcal vaccine (PPV23) in elderly persons. Since 2014, the Japanese government has offered subsidies through a 5-year national routine vaccination program for elderly persons at 5-year age intervals. Here, we investigated the effect of the national routine vaccination program on PPV23 vaccination rates. PPV23 vaccination rates were calculated as follows: cumulative amount shipped to each municipality divided by the population aged ≥65 years. At the end of 2015, 2 years into the 5-year national immunization program, the estimated vaccination rate was 40.6%, which was significantly increased compared with former periods (p = 0.01). Our findings show that the national routine vaccination program plays an important role in increasing the vaccination rate of PPV23 in Japan.