Remarkable progress in paediatric cardiology and surgery have led to the substantial increase of congenital heart disease (CHD) survivors. Long-term outcomes in rare and complex CHD have become a critical priority as three major sources of morbidity have been identified in this population: neurodevelopmental sequelae, mental health issues and reduced exercise capacity. These challenges adversely affect their quality of life and constitute a major public health issue. We seek to evaluate the efficacy of the first integrative and holistic program in Neuro-Cardiac Health associating physical and psychological rehabilitation for children with rare CHD compared to the standard of care. Children randomly assigned to the intervention will undergo a 12-week neuro-cardiac intervention including home-based adaptive physical exercise, telehealth parent and child psycho-education and child computerized cognitive training, as well in-person individual sessions of intervention reinforcement. Parents will be actively involved and will receive personalized feedback and educational resources. Children assigned to the control group will receive the standard of care in congenital cardiology. Post-intervention effects will be measured after 12-months on several outcomes including health-related quality of life (HRQoL), trained and untrained cognitive skills, mental health outcomes and cardiovascular/physical variables.