Background There is a growing population of palliated and unpalliated single ventricle physiology patients for whom heart transplantation is the only treatment option available. There is a paucity of reports of heart transplantation in this challenging and growing subset of patients from our part of the world. The purpose of the article is to briefly review our experience in the subgroup and compare it with the available literature. Methods This was a single-institution retrospective observational study of 16 patients with single ventricle physiology who were transplanted between 2016 and 2019 and their outcomes. The study groups were divided into those with ventricular dysfunction (group 1), who fare substantially better than those with normal ventricular function (group 2) whose short-term outcomes were poorer. Worsening cyanosis, poor candidature for completion Fontan procedure due to severe atrioventricular valve regurgitation or pulmonary artery anatomy, protein-losing enteropathy, plastic bronchitis, and worsening systemic venous congestion are indications in those with normal ventricular function. Results Patients with ventricular dysfunction as the main indication had excellent early survival with no early mortality compared to 40% mortality in patients with normal ventricular function. Patients who survived to leave the hospital had however similar long-term outcomes. Two patients with protein-losing enteropathy resolved completely by one month. Normal ventricular function, pulmonary artery stenting, early Fontan failure (6 months), ascites, and need for desensitization were risk factors for early mortality. After the early acute phase of increased risk, the mortality risk plateaued off. Conclusion Transplantation in patients with single ventricle and ventricular dysfunction can be offered with a good early and late outcome. There is a need to have multi-institutional and multi-disciplinary collaboration along with work in basic sciences to better understand the effects of failed Fontan physiology with normal ventricular function.