Tobacco-free policy in Japan lags behind those of most developed countries. Evidence is required to promote strong implementation of existing policies. This study aimed to assess whether exposure to secondhand smoke (SHS) influences the incidence of streptococcal infection in young children, to further support the need for effective tobacco-free policies in Japan. This study used medical administrative claim and health check data from the Japan Health Insurance Association Fukuoka branch. Participants were beneficiaries' dependents younger than age 4 years. Exposure was defined as SHS from beneficiaries' smoking, each year during 2011-2014. The outcome was incidence of streptococcal infection, diagnosed with and without laboratory testing. Logistic regression analysis was performed to yield odds ratios (ORs) of associations with the outcome and 95% confidence intervals (CIs). This study included a total of 5743 children. The proportion of all participants with a record of streptococcal infection was 4.2% (n = 244). The results of logistic regression analysis between streptococcal infection and SHS exposure showed a significantly higher association (OR 1.39, 95% CI 1.07-1.80, P < 0.05) if all cases were included and an insignificant association with diagnoses using testing (OR 1.20, 95% Cl 0.80-1.80, P = 0.39). This study showed that 60% of streptococcal infections in young children were diagnosed without testing, and SHS increased this incidence regardless of testing. It reports new findings regarding the effect of SHS on infection in young children to support implementation and promotion of tobacco-free policies by the Japanese government not only in public spaces, but also at home.