Children with congenital diaphragmatic hernia (CDH) suffer from long-term pulmonary morbidity. Longitudinal data of exercise capacity in these children are lacking. We hypothesized that exercise capacity would be impaired in children with CDH and deteriorates over time. We evaluated exercise capacity and its determinants in CDH patients longitudinally until 12 years of age. Prospective longitudinal follow-up study in tertiary university hospital. One hundred and fourteen children with CDH born between 1999 and 2012. Exercise capacity was evaluated using the Bruce treadmill-protocol at the ages of 5, 8, and 12 years. Primary outcome parameter was standard deviation score (SDS) of maximal endurance time. Data were analyzed by using linear mixed models. A total of 107 children (30 treated with extracorporeal membrane oxygenation [ECMO]) performed 191 reliable exercise tests. At ages 5, 8, and 12 years, the mean (95%CI) SDS endurance time was -0.44 (-0.65 to -0.24); -1.01 (-1.23 to -0.78); -1.10 (-1.40 to -0.80), respectively, all less than zero (P < 0.001). Exercise capacity declined significantly over time irrespective of ECMO-treatment (5-12 years: non-ECMO P = 0.015; ECMO P = 0.006). Duration of initial hospital stay and diffusion capacity corrected for alveolar volume were associated with SDS endurance time (P < 0.001 and P = 0.039). In CDH patients exercise capacity deteriorates between 5 and 12 years of age, irrespective of ECMO-treatment. CDH patients may benefit from long-term assessments of exercise capacity with timely intervention. © 2019 The Authors. Pediatric Pulmonology Published by Wiley Periodicals, Inc.