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The Fontan procedure (FP) is the standard surgical treatment for Univentricular heart diseases. Over time, the Fontan system fails, leading to pathologies such as protein-losing enteropathy (PLE), plastic bronchitis (PB), and heart failure (HF). FP should be considered as a transitional step to the final treatment: heart transplantation (HT). This systematic review and meta-analysis aims to establish the risk of death following HT according to the presence of FP complications. There was a total of 691 transplanted patients in the 18 articles, immediate survival 88% (<i>n</i> = 448), survival from 1 to 5 years of 78% (<i>n</i> = 427) and survival from 5.1 to 10 years of 69% (<i>n</i> = 208), >10 years 61% (<i>n</i> = 109). The relative risk (RR) was 1.12 for PLE (95% confidence interval [CI] = 0.89–1.40, <i>p</i> = 0.34), 1.03 for HF (0.7–1.51, <i>p</i> = 0.88), 0.70 for Arrhythmias (0.39–1.24, <i>p</i> = 0.22), 0.46 for PB (0.08–2.72, <i>p</i> = 0.39), and 5.81 for CKD (1.70–19.88, <i>p</i> = 0.005). In patients with two or more failures, the RR was 1.94 (0.99–3.81, <i>p</i> = 0.05). After FP, the risk of death after HT is associated with CKD and with the presence of two or more failures.