The prognosis of congenital heart disease is dramatically improved by cardiac surgery. The Fontan procedure is the definitive palliative operation for patients with single-ventricle physiology. In parallel with the longer survival time achieved with the Fontan procedure, the incidence of Fontan-associated liver disease is increasing. A 40-year-old man who underwent Fontan procedures at the ages of 9 was referred to our hospital for further evaluation of multiple hepatic tumors. Enhanced computed tomography showed large hepatocellular carcinomas with portal thrombi (Vp3). Spontaneous hepatocellular carcinoma rupture occurred 2 weeks after the first visit to our hospital, and emergent transcatheter arterial embolization of the hepatic artery was performed. Three months later, the patient died of liver failure. Autopsy findings showed moderately differentiated hepatocellular carcinoma with a cirrhotic liver characterized by centrilobular fibrosis and sinusoidal dilation similar to that in Fontan-associated liver disease. We reported the first case of spontaneously ruptured hepatocellular carcinoma treated by emergent transcatheter arterial embolization in Fontan-associated liver disease. As the early diagnosis of liver cirrhosis and hepatocellular carcinoma results in better patients' outcome, cardiologists and hepatologists should be aware of Fontan-associated liver disease and advise patients to have regular follow-up of the liver.