We report a case of bile leaks post-laparoscopic cholecystectomy (LC) with initial treatment failure by common bile duct stent insertion. The injury of a subvesical duct running from gallbladder fossa toward an area of fluid accumulation that was not revealed by computed tomography and endoscopic retrograde cholangiopancreatography previously, was eventually found by magnetic resonance cholangiopancreatography (MRCP) and proved to be the cause of bile leak. Also, several tiny branches in the right liver instead of a main trunk and another subvesical duct draining into the common bile hepatic duct was noted. These anatomic variations were scarcely reported, especially by MRCP. The aim of this case report is to discuss the link between biliary tree anomaly and bile leak due to bile duct injury during LC in our experience treating one patient. Also, we review related literature to understand more on prevention or management of subvesical duct injury.