This report presents the case of a 6-day-old male with cystic biliary atresia (CBA), and the cyst was detected antenatally. Antenatal ultrasonography suggested the possibility of CBA or a choledochal cyst at 16 weeks' gestation. However, the cyst disappeared during the later gestational period. The cyst was detected again by preoperative imaging. Surgical cholangiography at 30 days of age confirmed CBA, but the common hepatic duct (CHD) was extremely narrow. The histopathological findings revealed the partial obstruction of CHD. These findings suggest that correctable CBA (I cyst) may change into uncorrectable CBA (IIId).