Oesophageal atresia (EA) is associated with life-long gastrointestinal and respiratory morbidity and other associated malformations. The aim of this study is to compare physical activity (PA) levels of children and adolescents with and without EA. A validated questionnaire (MoMo-PAQ) was used to evaluate PA in EA patients EA (4–17 years), who were randomly matched for gender and age (1:5) with a representative sample of the Motorik-Modul Longitudinal Study (n= 6233). Sports activity per week (sports index) and minutes of moderate to vigorous physical activity per week (MVPA minutes) were calculated. Correlations between PA and medical factors were analysed. In total, 104 patients and 520 controls were included. Children with EA were significantly less active at higher intensities (mean MPVA minutes 462; 95% confidence interval (CI): 370–554) compared to controls (626; 95% CI: 576–676), although there was no statistically significant difference in the sports index (187; 95% CI: 156–220 versus 220; 95% CI: 203–237). A lower mean weight-for-age and height-for-age, additional urogenital (r=  − 0.20,p= 0.04) or anorectal malformation (r=  − 0.24,p= 0.01) were associated with fewer MVPA minutes. For other medical factors (prematurity, type of repair, congenital heart disease, skeletal malformation or symptom load), no statistically significant association with PA was found.Conclusion: EA patients participated in PA at a similar level but lower intensities compared to the reference cohort. PA in EA patients was largely independent of medical factors.Trial registration: German Clinical Trials Register (ID: DRKS00025276) on September 6, 2021.What is Known:•Oesophageal atresia is associated with a low body weight and height, delayed development of motor skills and impaired lung function and exercise capacity.What is New:•Patients with oesophageal atresia have a similar amount of sports activity per week but engage significantly less in moderate to vigorous physical activities compared to peers.•Physical activity was  associated with weight-for-age and height-for-age, but largely independent of symptom load and other medical factors.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00431-023-04923-3.