The aim of the study was to examine the effects of exercise training on aerobic capacity and pulmonary function in children and adolescents after congenital heart disease surgery. We searched MEDLINE, Cochrane Controlled Trials Register, EMBASE, (from the earliest date available to January 2015) for controlled trials that evaluated the effects of exercise training on aerobic capacity and pulmonary function (forced expiratory volume in 1 s and forced vital capacity) in children and adolescents after congenital heart disease surgery. Weighted mean differences and 95 % confidence intervals (CIs) were calculated,, and heterogeneity was assessed using the I 2 test. Eight trials (n = 292) met the study criteria. The results suggested that exercise training compared with control had a positive impact on peak VO2. Exercise training resulted in improvement in peak VO2 weighted mean difference (3.68 mL kg−1 min−1, 95 % CI 1.58–5.78). The improvement in forced expiratory volume in 1 s and forced vital capacity after exercise training was not significant. Exercise training may improve peak VO2 in children and adolescents after congenital heart disease surgery and should be considered for inclusion in cardiac rehabilitation. Further larger randomized controlled trials are urgently needed to investigate different types of exercise and its effects on the quality of life.