Abstract Background The age-specific distribution of SARS-CoV-2 cases in schools is not well described. Reported statistics reflect the intensity of community transmission while being shaped by biases from age-dependent testing regimes, as well as effective age-specific interventions. A case surveillance system was introduced within the Flemish school and health-prevention network during the 2020–2021 school year. We present epidemiological data of in-school reported cases in pre-, primary and secondary schools identified by the case surveillance system, in conjunction with test data and community cases from October 2020 to June 2021. Methods We describe the development of the surveillance system and provide the number of reported cases and standardized rates per grade over time. We calculated absolute and relative differences in case incidence according to school grade (primary: grades 1–6, and secondary: grades 7–12) using grades 7–8 as a comparator, relating them to non-pharmaceutical infection prevention ...