A 29-year-old woman who underwent the Fontan procedure at 10 years of age had an incidental finding of liver masses on abdominal ultrasonography. Subsequent gadolinium ethoxybenzyl diethylenetriamine pentaacetic acid magnetic resonance imaging showed a 15 mm hypervascular mass with washout in the hepatobiliary phase in liver segment 4 (S4), and an 18 mm hypervascular mass without washout in the hepatobiliary phase in liver segment 2 (S2). The S2 liver mass was pathologically diagnosed to be a regenerative nodule by an ultrasound-guided needle biopsy, and the S4 liver mass was pathologically diagnosed as a poorly differentiated hepatocellular carcinoma after partial hepatectomy.