Introduction: Without participating in a contractile chamber, the Fontan procedure seeks to create a separation of oxygenated and deoxygenated blood in patients with univentricular heart, reducing the risks of long-term hypoxemia and improving their survival. This study describes the clinical outcomes of children undergoing the Fontan procedure between 2000 and 2020 in a tertiary referral hospital care centre in southwestern Colombia. Materials and methods: A retrospective observational descriptive study. The 81 patients who underwent the Fontan procedure were included. Categorical variables were presented with percentages and continuous variables with measures of central tendency according to the distribution of the data evaluated through the Shapiro–Wilk test. Sociodemographic, clinical, surgical variables, complications, and mortality were described. Results: Between 2000 and 2020, 81 patients underwent the Fontan procedure: 43 (53.1%) males and a median age of 5.3 years (interquartile range 4.3–6.6). The most common diagnosis was tricuspid atresia (49.4%). The median mean pulmonary arterial pressure was 12 mmHg (interquartile range 10–15), the Nakata index 272 mm2/m2 (interquartile range 204–327), and the McGoon index (interquartile range 1.86–2.3). Seventy-two (88.9%) patients underwent extracardiac Fontan and 44 (54.3%) patients underwent fenestration. The median hospitalisation days were 19 days. The main complication was coagulopathy (19.8%), mortality in the first month between 2000 and 2010 was 8.6%, and after 2010 was 1.2%. Conclusion: The Fontan procedure is a palliative surgery for children with complex heart disease. According to anatomical and physiological variables, the proper choice of patients determines the short- and long-term results.