Choledochal cysts are a congenital disorder of the bile duct, usually presenting in childhood. As they cause weakening of the wall of the bile duct, any distal obstruction, infection or reflux of amylase-rich fluid in the biliary tract can predispose to spontaneous perforation. A 25-year-old pregnant woman at 35 weeks of gestation presented with acute abdominal and fetal distress. On emergency laparotomy, common bile duct perforations were detected. T-tube drainage and caesarean section were performed. A t-tube cholangiogram revealed the diagnosis of a choledochal cyst with an abnormal pancreatobiliary junction and chronic pancreatitis. The patient later underwent cyst excision with Roux en Y hepaticojejunostomy. Spontaneous choledochal cyst perforation in pregnancy can be successfully managed by a two-stage operation.