Choledochal cysts (CCs) are rare congenital anomalies in the form of cystic dilatation of any part of the biliary tree, and they rarely reach the size over 10 cm. We present a case of a 51-year-old female with a one-year history of abdominal pain and palpable mass in the epigastrium and right upper abdomen. Diagnosis of giant CC was made using magnetic resonance cholangiopancreatography. Intraoperatively, a large CC without gallbladder (no previous cholecystectomy was performed) was found under the liver pushing the surrounding structures, extending into the intrapancreatic portion of bile ducts and leading to the destruction of the backside of the pancreas head. Complete excision of CC and biliopancreatic reconstruction was achieved by Roux-en-Y pancreaticojejunostomy and hepaticojejunostomy. This case report describes an extremely rare association between an atypical giant choledochal cyst and gallbladder agenesis.