Heart transplantation (HT) as primary therapy for children with congenital heart disease (CHD) has become unusual. With improved early results of reconstructive surgery, the population of children and adults surviving with CHD is expanding. End-stage CHD related to myocardial dysfunction or circulation failure after prior surgery is becoming more common as an indication for HT. This heterogeneous group of CHD recipients referred for HT presents unique decision-making, technical, and physiologic challenges. Historically, a diagnosis of CHD has been a major risk factor for early mortality after HT. Rescue HT, especially in the setting of failing Fontan physiology, has the worst outcome. Early referral (before end-organ damage), proper selection, and optimization of recipients, as well as meticulous intra- and postoperative management are crucial to improving early outcomes of HT in this population. Beyond the early post-HT period, children with end-stage CHD experience long-term survival comparable to most other non-CHD recipients.