Objective To compare the aerobic and anaerobic exercise capacity of children with juvenile idiopathic arthritis (JIA) with healthy controls, to determine if there were differences based on disease onset type, and to examine the relationship between aerobic and anaerobic exercise capacity in children with JIA. Methods Sixty‐two patients with JIA (mean ± SD age 11.9 ± 2.2 years, range 6.7–15.9) participated in this study. Aerobic exercise capacity was measured using a cardiopulmonary exercise test. Anaerobic exercise capacity was measured using the Wingate Anaerobic Exercise Test (WAnT). Results All patients were able to perform the cardiopulmonary exercise test and WAnT without adverse events. On average, the maximal oxygen uptake (VO2peak) and VO2peak/kg were 69.8% and 74.8%, respectively, of that predicted compared with healthy controls. Mean ± SD power was 66.7% ± 37.2% of that predicted compared with healthy children. Mean ± SD peak power was 65.5% ± 43.1% of that predicted compared with healthy children. There were significant differences between subgroups of JIA; the oligoarticular‐onset group values did not significantly differ from healthy control values; the polyarticular rheumatoid factor positive–onset subgroup had the greatest impairment in both aerobic and anaerobic exercise capacity. The correlations of mean power and peak power with VO2peak were r = 0.884 and r = 0.697, respectively (P < 0.05). Conclusion This study demonstrates that both the aerobic and anaerobic exercise capacity in children with JIA are significantly decreased. The WAnT might be a valuable adjunct to other assessment tools in the followup of patients with JIA.