SummaryBackground and AimsThe Fontan palliation is the final stage of surgery for many children born with univentricular physiology. Almost all Fontan patients develop liver fibrosis which may eventually lead to cirrhosis and hepatocellular carcinoma (HCC). These are important causes of morbidity and mortality in these patients. We performed a systematic review and meta‐analysis to assess the incidence of cirrhosis and HCC in Fontan patients and stratify it based on time since surgery.MethodsA literature search of seven databases identified 1158 records. Studies reporting the number of cirrhosis and HCC cases in Fontan patients and time since Fontan surgery were included. In the cirrhosis cohort, we included only those studies where all patients underwent liver biopsy.ResultsA total of 23 studies were included: 12 and 13 studies in the cirrhosis and HCC cohorts, respectively, with two studies included in both cohorts. The incidence of cirrhosis was 0.97 per 100 patient‐years (95% CI 0.57–1.63), with the incidence and cumulative incidence ≥20 years post Fontan surgery being 1.61 per 100 patient‐years (95% CI 1.24–2.08) and 32.2% (95% CI 25.8%–39.4%), respectively. The incidence of HCC was 0.12 per 100 patient‐years (95% CI 0.07–0.21), with the incidence and cumulative incidence ≥20 years post Fontan surgery being 0.20 per 100 patient‐years (95% CI 0.12–0.35) and 3.9% (95% CI 2.2%–6.8%), respectively. Only about 70% of patients with HCC (20/28) had underlying cirrhosis.ConclusionThe incidence of cirrhosis and HCC increases over time, especially at ≥20 years post Fontan surgery. Studies are needed to further identify at‐risk patients in order to streamline surveillance for these highly morbid conditions.