Choledochal cysts are rare congenital or acquired cystic dilatations of the intra- or extrahepatic bile ducts. Their exact pathophysiology remains unclear. Extensive complications exist with untreated cysts. including biliary stasis and inflammation, with resultant stricture and stone formation, cholangitis, pancreatitis, and malignant degeneration. Most commonly reported malignancies include cholangiocarcinoma, adenocarcinoma, and gallbladder cancer. We report the case of a 41-year-old female with a history of chronic calcific pancreatitis, choledocholithiasis, and a large type I choledochal cyst, who presented with flu-like symptoms followed by painless jaundice and weight loss. Endoscopic retrograde cholangiopancreatography and direct cholangioscopy revealed a mass at the biliary bifurcation, a 4-cm choledochal cyst with multiple calculi, absence of anomalous pancreaticobiliary ductal union, and multiple calcifications in the pancreatic head. Pathology demonstrated a synchronous choledochal cyst and squamous cell carcinoma, an infrequently reported phenomenon. We report the associated rare finding of chronic calcific pancreatitis, without anomaly of the pancreatic biliary junction. This suggests that the formation of calculi within the choledochal cyst may contribute to chronic calcific pancreatitis, possibly by virtue of papillary stenosis.