The implementation of COVID-19 pandemic-related restrictions resulted in limitations for physical activity (PA) opportunities, which may have initiated a longer-term behavioural change. The protocol describes the methodology for a planned systematic review that aims to summarise changes in PA and physical fitness (PF) in children and adolescents in the WHO European Region after the onset of the COVID-19 pandemic. Ethical approval is not required, as primary data will not be collected in this study. The results will be presented in a peer-reviewed publication and at congresses relevant to the research field.