Choledochal cysts are rare congenital malformations of the bile duct characterized by dilatations of the intrahepatic and/or extrahepatic portion of the biliary tree, they are associated to an anomalous arrangement of the pancreaticobiliary duct. Pancreas divisum results from a fusion failure of the pancreatic buds. The coexistence of pancreas divisum and choledochal cyst in adults has been reported in less than 10 well documented cases. This article presents a case of a 42-year-old Peruvian man with intermittent episodes of abdominal pain, initially diagnosed with choledocholithiasis, who underwent open cholecystectomy. During surgery, a diagnosis of choledochal cyst and pancreas divisum was made, and therefore a hepaticoduodenostomy was performed. The patient was referred to our hospital due to persistence of abdominal pain. After admission, a papillectomy was achieved without further complications. A cyst resection and dismantling of hepaticoduodenostomy with Roux-en-Y was performed 8 years later. During the subsequent 18-month follow-up, the patient remains asymptomatic.