Choledocholithiasis after cholecystectomy is a clinically significant cause of recurrent biliary symptoms and may result from retained stones, recurrent stone formation, or calculi within the cystic duct remnant. Although uncommon, cystic duct stump calculi can present several years after surgery and may be associated with chronic inflammation, adhesions, and, rarely, biliary fistula formation. We report the case of a 48-year-old female with a history of open cholecystectomy who presented with recurrent right upper abdominal pain, intermittent jaundice, clay-colored stools, and high-colored urine. Magnetic resonance cholangiopancreatography (MRCP) revealed choledocholithiasis with proximal biliary dilatation, along with a cystic duct stump calculus. The patient was planned for choledochoduodenostomy; however, intraoperative findings included dense adhesions, a cystic duct remnant-common bile duct (CBD) fistula, and an impacted stump stone, making the planned procedure unsafe. The surgical approach was modified, and CBD exploration with stone extraction and T-tube drainage was performed. The postoperative course was uneventful, and a T-tube cholangiogram confirmed satisfactory ductal clearance. The patient remained asymptomatic on follow-up, with normalization of liver function tests. This case highlights the importance of considering cystic duct stump pathology in post-cholecystectomy patients with recurrent biliary symptoms and underscores the need for individualized surgical decision-making in complex reoperative biliary surgery.