Background: The Fontan procedure is a palliative surgical strategy for patients with single-ventricle congenital heart disease. Although surgical advances have improved survival, Fontan patients remain exposed to multiple late complications, including arrhythmias, thromboembolic events (TE), protein-losing enteropathy (PLE), and liver disease. Purpose: To evaluate long-term clinical outcomes in adult Fontan patients and to explore the impact of Fontan surgical techniques and underlying congenital defects on prognosis. Methods: We conducted a single-center retrospective cohort study using data from the institutional Fontan Registry between January 2005 and December 2023. Seventy-seven adult patients with a minimum follow-up of two years after Fontan completion were included. Data on surgical history, complications, antithrombotic therapy, hospitalizations, and survival were analyzed. Results: The cohort included 77 patients (mean age 31.6 ± 9.6 years, 58% male). Tricuspid atresia was the most frequent diagnosis (38%), followed by double-inlet left ventricle (13%). Total cavopulmonary connection with extracardiac conduit was performed in 69%. Arrhythmias were the most common complication (43%), particularly in atriopulmonary connections. TE occurred in 18%, mainly intracardiac thrombosis and pulmonary embolism. TE rates were higher in patients not receiving antithrombotic therapy (43%) compared with those on aspirin or anticoagulation. Hemorrhagic complications occurred in 19%, with major bleeding in 5%. PLE was diagnosed in 12% of patients, requiring repeated hospitalizations. Liver disease, including fibrosis or cirrhosis, was detected in 39%. Among female patients, 15% experienced pregnancy, with one arrhythmic complication requiring cardioversion. The annual hospitalization rate was 0.236 per patient-year. Overall mortality was 9%, mainly related to heart failure and PLE. Conclusions: Despite improved survival, adult Fontan patients remain burdened by significant long-term morbidity. Arrhythmias and thromboembolic events have a major impact on prognosis, while liver disease and PLE contribute to hospitalizations and disease complexity. These findings emphasize the importance of lifelong, multidisciplinary follow-up, careful risk stratification, and individualized management strategies to improve outcomes and quality of life in this growing population.