Background: While exercise training is beneficial in the prevention and management of many chronic diseases, the role of exercise training in children and adolescents with congenital heart disease is less understood. We sought to determine the safety and efficacy of exercise training in children and adolescents with congenital heart disease. Methods: We conducted a systematic search of the following databases: PubMed, CINAHL, EMBASE, Web of Science and SportDiscus. We included randomised controlled trials that incorporated an exercise intervention compared with a non-exercising comparator group and examined safety and efficacy in children and adolescents with congenital heart disease. A descriptive analysis of the included trials was then conducted. Results: A total of 9 articles from 6 trials (642 participants with varying conditions and disease severity) were included. Significant variability of study participants and outcomes were observed across the trials. No adverse events linked to the exercise interventions were stated. The articles reported numerous positive changes to clinically relevant fitness measures. Exercise capacity improved with exercise training in 3 of 4 trials in which it was measured. Cardiorespiratory fitness showed improvements in 3 of 4 trials. Neuromuscular fitness increased in 1 of 2 trials. Physiological and metabolic parameters were improved, and negative changes were not observed to several clinically important measures (e.g. muscular oxygenation, cardiac measures) in 2 of 2 trials. Physical activity increased in 1 of 3 trials. No articles reported on changes in measures of body composition. Outcomes are varied with little consensus on measurements or assessment methods. Conclusions: Exercise training appears to be safe and efficacious for improving physical fitness in children and adolescents with congenital heart disease who have been appropriately screened by their medical team. However, the certainty of the evidence for these findings is low to moderate.