A 2-month-old boy with biliary atresia (BA) with an extremely rare prenatal history is reported. A cystic lesion in the hepatic hilum was diagnosed during prenatal ultrasonography at 20 weeks' gestation. However, it disappeared during later prenatal observation. He was diagnosed with an uncorrectable type of BA after a massive subdural hemorrhage at the age of 66 days. A fetus suspected of having a cyst of the biliary tree should be followed even after the cyst has disappeared spontaneously.