Background Patients with failing Fontan circulation are at high risk for complications after heart transplantation (HTx) because of multiple prior operations, elevated panel reactive antibody, hepatic dysfunction, coagulopathy, protein-losing enteropathy (PLE), and poor nutrition. The purpose of this review was to evaluate the outcome of HTx for these patients, including those who are status post-Fontan conversion. Methods Of 206 heart transplants at Ann & Robert H. Lurie Children's Hospital of Chicago from 1990 to 2012, 22 patients had a failing Fontan. Median age at HTx was 12.2 years, median interval from initial Fontan to HTx was 7.1 years. Potential preoperative risk factors included PLE (n = 15), mechanical ventilation (n = 8), prior Fontan conversion (n = 7), renal failure (n = 3), and plastic bronchitis (n = 2) Median number of prior operations was 3. Donor branch pulmonary arteries were used in 17 patients. Results There were 5 early deaths (23%), due to graft failure (1), pulmonary hypertension (1), and infection (3). There were 3 late deaths (13%) at 1, 5, and 8 years. Two of 3 patients with preoperative renal failure died. Survivors who had preoperative PLE (n = 11) and preoperative plastic bronchitis (n = 2) experienced complete resolution of these pathological conditions after heart transplantation. Median length of stay was 30 days. Five of 7 Fontan conversion patients survived, and 6 of 8 preoperative ventilator-dependent patients survived. One-, 5-, and 10-year survival was 77%, 66%, and 45%, respectively. Conclusions The operative mortality of HTx for patients with a failing Fontan is high. Using the donor branch pulmonary arteries greatly facilitated the transplant. Because infection caused the majority of early deaths, lower intensity initial immunosuppression may be warranted. Transplantation was successful in treating PLE in all survivors. Prior Fontan conversion was not a risk factor. Preoperative mechanical ventilation was not a risk factor. Preoperative renal failure may be a relative contraindication. Earlier referral of failing Fontan patients may improve results.