We report the case of a 20-year-old woman with a complex type “D” pancreaticobiliary maljunction and recurrent pancreatitis who underwent surgical resection with Roux-en-Y reconstruction. Fourteen years later, magnetic resonance cholangiopancreatography (MRCP) revealed dilation of the common bile duct with associated stones. Endoscopic retrograde cholangiopancreatography (ERCP) with sphincterotomy was performed to confirm the MRCP findings and facilitate stone removal; this procedure also demonstrated an incomplete pancreas divisum. Given the complex postoperative anatomy and the long-standing history of inflammation, direct cholangioscopy was used to inspect the biliary epithelium, clarify the anatomy, and enable selective cannulation. In this setting, ERCP combined with direct cholangioscopy represented a reliable approach for the postoperative management of maljunction, offering a minimally invasive option for surveillance while improving anatomical assessment and guiding subsequent management.