BACKGROUND Extra-hepatic bile duct injury (EHBDI) is very rare among all blunt abdominal injuries. According to literature statistics, it only accounts for 3%-5% of abdominal injuries, most of which are combined injuries. Isolated EHBDI is more rare, with a special injury mechanism, clinical presentation and treatment strategy, so missed diagnosis easily occurs. CASE SUMMARY We report a case of unexplained abdominal effusion and jaundice following blunt abdominal trauma in our department. Of which, surgical exploration of the case was performed and a large amount of bile leakage in the abdominal cavity was found. No obvious abdominal organ damage or bile duct rupture was found. Surgery was terminated after the common bile duct indwelled with a T tube. After 2 wk, a T-tube angiography revealed the lesion in the common bile duct pancreatic segment, confirming isolated EHBDI. And 2 mo later, the T tube was pulled out with re-examined magnetic resonance cholangiopancreatography, indicating narrowing of the common bile duct injury, with no special treatment due to no clinical symptoms and no abnormality in the current follow-up. CONCLUSION This case was featured by intraoperative bile leakage and no EHBDI. This type of rare isolated EHBDI is prone to missed and delayed diagnosis due to its atypical clinical manifestations and imaging features. Surgery is still the main treatment, and the indications and principles of bile duct injury repair must be followed.