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 interventions. Cumulative population incidences (IP) stratified by age, province and socioeconomic status (SES) of the school population are presented with their 95% confidence intervals (CI). Results A total of 59,996 COVID-19 cases were reported in the school surveillance system, with the highest population adjusted IP in grade 11–12 of 7.39% (95%CI 7.24–7.53) and ranging from 2.23% to 6.25% from pre-school through grade 10. Age-specific reductions in mask introduction and in-person teaching were temporally associated with decreased case incidence, while lower pupil SES was associated with an increase in cumulative cases (excess 2,739/100,000 pupils compared to highest SES tertile). Community testing volumes varied more for children compared to adults, with overall higher child test-positivity. Holidays influence capturing of cases by the system, however efficiency increased to above 75% after further automation and integration in existing structures. Conclusion We demonstrate that effective integration of ...