Objectives: Fontan circulation presents significant challenges for patients with congenital heart disease, often necessitating heart transplantation (HTX) due to deteriorating functionality across multiple organ systems. However, the impact of prior Fontan palliation on HTX outcomes remains poorly understood, with early mortality rates suggesting a heightened risk. The aim of our study is to evaluate the long-term results after heart transplantation in patients with univentricular congenital heart disease previously palliated with Fontan circulation. Methods: A retrospective analysis was conducted on patients who underwent HTX for congenital heart disease. Patients were categorized into two groups based on the pre-HTX circulation pathway: the Failing Fontan Group (FFG) and the Biventricular Congenital Group (BCG). Data were collected from patients between 1987 and 2018. Early and late outcomes, including survival rates, were assessed and critically analyzed. Results: Of the 66 patients, 29 (43%) had a failing Fontan palliation (FFG), and 37 had biventricular congenital diseases (BCG) before heart transplantation. Early mortality (30-day) was not statistically different between the two group. The overall survival rate was 82.6 ± 13.9% at 1 year, 79.0 ± 14.9% at 5 years, 67.2 ± 17.6% at 10 years and 63.2 ± 18.2 ± at 15 years for the FFG, and 86.1 ±11.4% at 1 year, 79.5 ± 13.7% at 5 years, 75.7 ± 14.9% at 10 years, 75.7 ± 14.9% at 15 years for the BCG, with no statistically significant difference (Mantel Cox p value: 0.69, 0.89, 0.52 and 0.39, respectively). Regarding Cox-regression analysis, the long-term survival rate was not affected either by previous Fontan surgery or by the era of heart transplantation (before vs. after the year 2000). Conclusions: Although heart transplantation after Fontan palliation showed a higher risk in the early post-operative period, the medium- and long-term survival rates are comparable with biventricular circulation patients. Despite the failing Fontan patients being a challenging set of candidates for transplantation, it is a reasonable option in their treatment.