Objectives Patients may develop liver dysfunction, including liver fibrosis, over the long term following Fontan procedure. Therefore, early detection of liver dysfunction is essential to identify those patients who are at risk. We evaluated various laboratory parameters, including liver biochemical markers, hepatic echography findings, and cardiac catheterization outcomes, at an early stage after undergoing Fontan procedure. Methods A total of 56 patients who underwent Fontan procedure were included in the study. All patients underwent cardiac catheterization and biochemical markers were evaluated from the samples. Abdominal echography was performed on a subgroup of patients (n = 20) to observe the structure of liver tissues and to measure blood flow in the hepatic vein, portal vein, and hepatic artery. Results The mean period of time since Fontan procedure was 2.8 ± 2.1 years. There was a significant correlation between venous pressure and serum levels of γ-glutamyltranspeptidase and type IV collagen 7s domain, which indicated a high probability of liver consolidation. The other biochemical markers were normal. Stepwise regression analyses suggested that by using the ratio of hepatic venous flow and type IV collagen 7s collagen domain concentration, inferior vena cava pressure can be predicted. Conclusions Our study showed that we can predict inferior vena cava pressure using noninvasive abdominal echography and biochemical markers at an early stage after Fontan procedure.