The authors describe a rare case of choledochal cyst and aplasia of the dorsal pancreas complicated with chronic pancreatitis. A 9-year-old boy presented with obstructive jaundice. After biliary drainage using pericutaneous transhepatic gallbladder drainage (PTGBD) technique, the patient underwent choledochal cyst excision with Roux-en-Y hepaticojejunostomy. The association of choledochal cyst and aplasia of the dorsal pancreas with chronic pancreatitis has never been reported previously.