Abstract Background Following a first wave in spring and gradual easing of lockdown, Luxembourg experienced an early second epidemic wave of SARS-CoV-2 before the start of summer school holidays on 15th July. This provided the opportunity to investigate the role of school-age children and school settings for transmission. Methods We compared the incidence of SARS-CoV-2 in school-age children, teachers and the general working population in Luxembourg during two epidemic waves: a spring wave from March–April 2020 corresponding to general lockdown with schools being closed and May–July 2020 corresponding to schools being open. We assessed the number of secondary transmissions occurring in schools between May and July 2020 using routine contact tracing data. Results During the first wave in March–April 2020 when schools were closed, the incidence in pupils peaked at 28 per 100,000, while during the second wave in May–July 2020 when schools were open, incidence peaked 100 per 100,000. While incidence of SARS-CoV-2 was higher in adults than in children during the first spring wave, no significant difference was observed during the second wave in early summer. Between May and July 2020, we identified a total of 390 and 34 confirmed COVID-19 cases among 90,150 school-age children and 11,667 teachers, respectively. We further estimate that 179 primary cases caused 49 secondary cases in schools. While some small clusters of mainly student-to-student transmission within the same class were identified, we did not observe any large outbreaks with multiple generations of infection. Conclusions Transmission of SARS-CoV-2 within Luxembourg schools was limited during an early summer epidemic wave in 2020. Precautionary measures including physical distancing as well as easy access to testing, systematic contact tracing appears to have been successful in mitigating transmission within educational settings.