Muscular and cardiorespiratory dysfunction contributes to exercise intolerance. Therefore, the aim of the present study was to characterize the cardiopulmonary response andrespiratory muscle oxygenation of children with congenital heart diseases (CHD) when compared with those of healthy children. Twelve children with CHD in New York Heart Association (NYHA) class II or III, and 14 healthy children participated in the study. All subjects performed conventional spirographic measurements and a cardiopulmonary exercise test on a cycle ergometer. Oxygen uptake (VO2), carbon dioxide production (VCO2), minute ventilation (VE), heart rate (HR), and power output were measured. Oxygenation of respiratory muscles was assessed by near-infrared spectroscopy (NIRS) during exercise and recovery. Pulmonary function was normal and no significant difference was found between groups. At rest, CHD patients had cardiorespiratory variables comparable with those of the healthy group. At submaximal intensity (ventilatory threshold) and at peak exercise, power output, HR, VO2, VCO2, and VE were significantly reduced (p < 0.01) in CHD patients. Respiratory muscles deoxygenated during exercise in both groups. However, deoxygenation was more pronounced in the CHD group than in the healthy children from an intensity of 40% up to exhaustion. Likewise, children with CHD showed a slower recovery of oxygenation than healthy children (113.4 ± 17.5 vs. 74.6 ± 13.0 s; p < 0.001). Compared with healthy children, these results demonstrated that children with CHD have reduced performance and present a defected exercise capacity. Children with CHD showed a more pronounced decrease of respiratory muscle oxygenation and slower recovery of oxygen kinetics.