We report a case of 14-year-old male patient who underwent bile-duct-to-jejunum anastomosis because of congenital biliary atresia at the age of 2 months. A 15 mm hypervascular nodule was detected for the first time in the S1 region of the liver at the age of 9 years. Two years later, 6 hypervascular nodules were found in the liver. A tumor biopsy was performed. It was diagnosed as a focal nodular hyperplasia (FNH). However, the number of nodules increased from 6 to 12 and those diameters were enlarged two to seven times one year later; the tumor biopsy was performed again. Histologically, the findings were consistent with those obtained previously, which indicated FNH. We consider that this is a very rare case of FNH in which both the number of nodules and the size were increased in a short period of time. We present it here as a valuable case report.