Spontaneous perforation of the bile duct is a rare disease, and delayed diagnosis without optimal treatment can be fatal. Abdominal drainage with or without repair of perforation seems to be adequate in most case series. We report on a 10-day-old female neonate with spontaneous perforation of the bile duct over the junction of cystic duct and common hepatic duct, who recovered uneventfully with follow-up for 3 years after receiving a single-stage operation of cholecystectomy and biliary reconstruction. Drainage only or resection of the gall bladder or bile duct should depend on the patient's clinical conditions and intraoperative findings.