Currently, there is an increasing prevalence of liver nodules in patients following the Fontan operation. The appropriate non-invasive modalities have been applied to assess a diagnosis of Fontan-associated liver disease. The aims of this study were to determine the prevalence and associated factors for the presence of liver nodules using CT scan. A cross-sectional study of 34 patients older than 15 years of age was recruited. Ultrasound upper abdomen, ultrasound liver elastography, and CT scan of the upper abdomen were performed after the Fontan operation. The median age of patients was 20 years (range 14–36 years). The median age at the Fontan operation was 7 years (range 5–17 years) and the duration after the Fontan operation was 12 years (range 4–22 years). The prevalence of liver nodules was 62% as detected by CT scans. Hepatic vein pressure in patients with liver nodules was significantly higher than in those without liver nodules. Hepatic vein pressure above 13 mmHg was a factor associated with liver nodules. There was little agreement between the ultrasound of the upper abdomen and CT scan of the upper abdomen in the evaluation of liver nodules. Hepatic pressure was the only associated factor for the occurrence of liver nodules in patients following the Fontan operation. The prevalence of liver nodules was very high after the Fontan operation. The upper abdomen CT scan should be performed for the surveillance of liver nodules in every Fontan patient over the age of 15 years.