Non-pharmaceutical interventions (NPIs) imposed during the COVID-19 pandemic were known to create an immunity debt. This study aimed to quantify the immunity debt for respiratory syncytial virus (RSV), adenovirus, group A Streptococcus (GAS), and influenza in Japan between 2014 and 2024. We conducted a retrospective observational study using national surveillance data and electronic health records in 23 clinics. We conducted an interrupted time series analysis using a quasi-Poisson regression model to estimate the counterfactual incidence that would have occurred in the absence of NPIs. The number of RSV cases declined by 84% in the 2020–2021 season and increased by 39% in the 2021–2022 season, primarily due to an increase in cases among 2-year-old children (94%). Adenovirus, GAS, and influenza were suppressed during the 2020–2022 season by 58–99%. Adenovirus cases increased by 195% in 2023, with a 458% increase among children aged 5–9 years. GAS increased by 36% in 2024, with a 96% increase among 10- to 14-year-olds. Influenza increased by 158% in 2023, with a 299% increase among 10- to 14-year-olds. Surveillance data and 23 clinics’ data showed similar trends. The study suggests that the intensity and timing of the immunity debt differed by pathogen.