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Objectives To evaluate the risk of invasive pneumococcal disease (IPD) and non-bacteraemic pneumonia (NBP)/acute otitis media (AOM)/sinusitis in Japanese individuals under 19 years of age with chronic medical conditions (CMCs) compared with those without.Design An observational, retrospective, cohort study.Setting A large, longitudinal health insurance claims database in Japan (JMDC database).Participants A total of 12.3 million individuals aged <19 years identified between 2006 and 2022 were included in the analysis. Seventeen CMCs as well as IPD and NBP/AOM/sinusitis were identified using diagnostic codes from the International Statistical Classification of Diseases and Related Health Problems V.10.Primary outcome measure Adjusted incidence rate ratios (IRRs) for IPD and NBP/AOM/sinusitis for individuals with CMCs versus those without CMCs were calculated using multivariate Poisson regression models with age and sex as covariates.Results The incidence rate of IPD was higher in individuals with a CMC (0.9 (95% CI: 0.8 to 0.9)) than in those without (0.1 (95% CI: 0.1 to 0.1)). A similar trend was observed for the incidence rate of NBP/AOM/sinusitis, with rates of 928.7 (95% CI: 927.4 to 929.9) in individuals with a CMC compared with 433.2 (95% CI: 432.8 to 433.7) in those without. The risk of IPD increases with the number of CMCs. The IRRs for IPD for those with one CMC and with two or more CMCs were 7.2 (95% CI: 6.4 to 8.1) and 128.1 (95% CI: 114.8 to 143.0), respectively, compared with individuals without a CMC. The IRRs for IPD in the immunocompromised and immunocompetent groups were 156.1 (95% CI: 133.4 to 182.7) and 16.3 (95% CI: 14.6 to 18.1), respectively. The IRRs for NBP/AOM/sinusitis were 1.9 (95% CI: 1.9 to 1.9) and 2.1 (95% CI: 2.1 to 2.2) for individuals with one CMC and with two or more CMCs, respectively.Conclusion Individuals aged <19 years with CMC are at higher risk of developing IPD and NBP/AOM/sinusitis, compared with those without. Our findings suggest the importance of vaccination against pneumococcal diseases in paediatric populations with CMCs.