Reported long-term outcome measures vary greatly between studies in Fontan patients making comprehensive appraisal of mortality hazard challenging. We sought to create a clinical risk score to assist monitoring of Fontan patients in the outpatient setting. A systematic review was conducted to evaluate risk factors for long-term (beyond the first postoperative year) mortality in Fontan patients. Studies were eligible for inclusion if ≥90 patients were included or ≥20 long-term mortalities we reported. Risk factors for long-term mortality were determined. The pooled hazard ratios were used to create components of a clinical score for long-term mortality using meta-analysis techniques. Twenty-eight studies were included. The total number of patients was 6707 with an average follow-up of 8.23 ± 5.42 years. There were 1000 deaths. Thirty-five risk factors for late mortality were identified and classified into 9 categories and their relative hazards were used to derive the initial components of a weighted, practical and clinically based Fontan risk score (ranging from 0 to 100). The final score included 8 risk factors: anatomic risk factors, elevated preoperative pulmonary artery pressure, atriopulmonary Fontan, heart failure symptoms, arrhythmia, moderate/severe ventricular dysfunction or atrioventricular valve regurgitation, protein losing enteropathy, and end organ disease (cirrhosis or renal insufficiency). In patients with Fontan circulation, the influence of readily available risk factors can be quantified in an integer score to predict long-term mortality. Prospective validation and refinement of this risk score will be undertake