We investigated the effect of training on peripheral muscular performance and oxygenation during exercise and recovery in children with congenital heart diseases (CHD). Eighteen patients with CHD aged 12 to 15 years were randomly assigned into either an individualized 12-week aerobic cycling training group (TG) or a control group (CG). Maximal voluntary contraction (MVC) and endurance at 50% MVC (time to exhaustion, T(lim)) of the knee extensors were measured before and after training. During the 50% MVC exercise and recovery, near-infrared spectroscopy (NIRS) was used to assess the fall in muscle oxygenation, i.e., deoxygenation ([Formula: see text]) of the vastus lateralis, the mean rate of decrease in muscle oxygenation, the half time of recovery (T(1/2R)), and the recovery speed to maximal oxygenation (R(S)). There was no effect of time on any parameter in the CG. After training, significant improvements were observed in TG for MVC (101.6 ± 14.0 vs. 120.2 ± 19.4 N·m, p < 0.01) and T(lim) (66.2 ± 22.6 vs. 86.0 ± 23.0 s, p< 0.01). Increased oxygenation (0.20 ± 0.13 vs. 0.15 ± 0.07 a.u., p < 0.01) and faster mean rate of decrease in muscle oxygenation were also shown after training in TG (1.22 ± 0.45 vs. 1.71 ± 0.78%·s(-1), p < 0.001). Moreover, a shorter recovery time was observed in TG after training for T(1/2R) (27.2 ± 6.1 vs. 20.8 ± 4.2 s, p < 0.01) and R(S) (63.1 ± 18.4 vs. 50.3 ± 11.4 s, p < 0.01). A significant relationship between the change in [Formula: see text] and both MVC (r = 0.95, p < 0.001) and T(lim) (r = 0.90, p < 0.001) in TG was observed. We concluded that exercise training improves peripheral muscular function by enhancing strength and endurance performance in children with CHD. This improvement was associated with increased oxygenation of peripheral muscles and faster recovery.