The frequency of major vascular injury encountered during the cholecystectomy procedure is very low. In the present case report, a congenital anomaly of portal vein is addressed. A 26-year-old female patient was admitted for urgent laparoscopic cholecystectomy due to a new episode of acute cholecystitis. She is already scheduled 2 times for elective cholecystectomy but canceled the surgery due to anxiety. The patient underwent laparoscopic cholecystectomy in the same day of admission. A major and rare case of intra-operative complication of portal vein injury during the laparoscopic cholecystectomy was encountered. The injury was well managed by suture repair. The vascular injuries may cause significant morbidity and sometimes mortality if not managed appropriately. Thus, our report may help to highlight the prompt management of vascular injuries at early stage.