Exercise capacity has been reported to be lower in children with Juvenile Idiopathic Arthritis (JIA). Therefore, the aim was to investigate the effects of an 8-week water-based exercise program on exercise capacity in children with JIA. Forty-two children with JIA were divided into two groups as: exercise group [n = 21, water-running, moderate-intensity exercise (60-70%), two times/week], and control group (n = 21, no additional treatment other than the prescribed medication). All children were assessed at baseline and post-intervention in terms of physical and disease-related characteristics, pain at rest and in activity (visual analog scale), range of motion (Escola Paulista de Medicina Range of Motion Scale), aerobic exercise capacity (cycle ergometer), and anaerobic exercise capacity (Wingate Test). Anaerobic exercise capacity was found to be improved in the exercise group [baseline: 5.54 W/kg (IQR 25/75: 4.07/6.88 W/kg) vs. post-intervention: 6.0 W/kg (IQR 25/75: 4.8/7.4 W/kg), p = 0.002], while no improvements were observed in the control group [baseline: 5.29 W/kg (IQR 25/75: 4.75/5.85 W/kg) vs. post-intervention: 5.5 watts/kg (IQR 25/75: 5.0/6.1 W/kg), p = 0.076]. The amount of the changes related to anaerobic exercise capacity were higher in the exercise group [exercise group: 0.6 W/kg (IQR 25/75: 0.3/1.3 W/kg) vs. control group: 0.2 W/kg (IQR 25/75: - 0.1/0.5 W/kg), p = 0.024]. No changes were detected related to aerobic exercise capacity in any of the groups (p > 0.05). An 8-week water-running program might be beneficial to improve anaerobic exercise capacity, but it is not enough to improve the aerobic exercise capacity in children with JIA.