SummaryIntroductionThe COVID‐19 pandemic posed tremendous challenges for children. However, the long‐term effects of the pandemic on various aspects of physical health at a national level remain unclear.MethodsIn this retrospective cohort study, we analysed data from nationwide health checkup records amongst children aged 7–15 years. The dataset comprised 3 544 146 records from 393 794 individuals who graduated from junior high school during fiscal years 2007 to 2022. Difference‐in‐differences (DID) analyses with multiple time periods were used to examine the impact of COVID‐19 on physical health outcomes.ResultsCompared with the pre‐pandemic period, the COVID‐19 pandemic was associated with excess increases in obesity for boys and girls, persisting over the 3 years (+0.42%; [95% CI, 0.23–0.61]). Also, it was associated with excess increases in underweight (+0.28% [0.25–0.32]) and poor visual acuity amongst boys in the 3rd year (+1.80% [1.30–2.30]). There were excess reductions in dental caries (−1.48% [−2.01 to −0.95]), glucosuria (−0.55 [−0.88 to −0.23]) and hematuria (−0.43% [−0.73 to −0.13]) during the 3rd year of the pandemic.ConclusionsThese findings underscore the multifaceted impact of the pandemic on various health indicators for school‐aged children. This information could be valuable for public health policy and paediatric healthcare planning in the post‐pandemic era.