Background: Certain congenital heart lesions in children can lead to irreversible lung disease thus making lung transplantation a therapeutic option. We retrospectively analyzed our experience with lung transplantation in 32 children with three distinct underlying congenital heart defects: (1) Eisenmenger syndrome (EIS); (2) tetralogy of Fallot with pulmonary atresia (PA); and (3) pulmonary vein stenosis (PVS). Methods: Pediatric patients <18 years of age with either EIS (n = 7), PA (n = 8) or PVS (n = 17), who underwent lung or heart-lung transplantation, were analyzed. We compared survival rates between the three groups. Pre- and peri-operative variables were also assessed for their effect on outcome. Results: Compared with EIS and PA patients, PVS patients were younger and sicker at the time of transplantation. All EIS and PA patients required either additional intracardiac repairs or a heart transplant at the time of lung transplantation. PA patients had the highest rate of major post-operative complications and in-hospital deaths. Median survival was comparable between EIS (6.1 years) and PVS (6.5 years) patients. Outcomes for PA patients were dramatically worse, with a median survival of only 0.12 year (∼47 days). Needing additional intracardiac surgery or a heart transplant at the time of lung transplantation did not impact survival. The diagnosis of PA itself correlated with a worse outcome. Conclusions: Outcomes in EIS and PVS patients undergoing lung transplantation compare favorably to that of all pediatric lung transplant recipients (median survival 4.3 years). For PA patients, their underlying pathology appears to make them high-risk candidates for lung transplantation. For the younger and acutely sicker PVS patients, lung transplantation is a viable therapeutic alternative.