To evaluate the moderating influence of parental variables on changes in health-related quality of life (HRQoL) in adolescents with Tetralogy of Fallot (ToF) or a Fontan circulation after participation in standardized exercise training. A multicenter randomized controlled trail in which 56 patients, aged 10-15, were randomly allocated (stratified by age, gender, and congenital heart disease) to a 12-week period with either: (a) 3 times per week standardized exercise training or (b) care-as-usual (randomization ratio 2:1). Adolescents and their parents filled in online questionnaires at baseline and at 12-week follow-up. In this randomized controlled trail, primary analyses involved influence of parental mental health and parental social support for exercise on changes in the TNO/AZL Child Quality of Life Questionnaire Child Form at follow-up. Secondary analyses concerned comparing levels of parental characteristics with normative data. Compared with controls, adolescents in the exercise group reported a decrease in social functioning when their parents had more anxiety/insomnia or severe depression themselves. Adolescents also reported a decrease in social functioning when their parents showed poorer overall mental health themselves. Parents reported comparable or even better mental health compared with normative data. The effect of a standardized exercise program on HRQoL changes in adolescents with ToF or a Fontan circulation is moderated by parental mental health, more specifically by parental anxiety/insomnia and severe depression. The trial registration number of this article is NTR2731 ( www.trialregister.nl ).