The literature on post-hepatectomy bile duct injury (PHBDI) is limited, lacking large sample retrospective studies and high-quality experience summaries. Therefore, we reported a special case of iatrogenic bile duct injury caused by Glissonean pedicle transection with endovascular gastrointestinal anastomosis (endo-GIA) during a right hepatectomy, analyzed the causes of this injury, and summarized the experience with this patient.We present the case of a 66-year-old woman with recurrent abdominal pain and cholangitis due to intrahepatic cholangiectasis (Caroli's disease). Preoperative evaluation revealed that the lesion and dilated bile ducts were confined to the right liver, with right hepatic atrophy, left hepatic hypertrophy, and hilar translocation. This problem can be resolved by performing a standard right hepatectomy. Although the operation went well, jaundice occurred soon after the operation. Iatrogenic bile duct injury was considered after magnetic resonance cholangiopancreatography review, and the second operation were performed 10 d later. During the second operation, it was found that the endo-GIA had damaged the lateral wall of the hepatic duct and multiple titanium nails remained in the bile duct wall. This led to severe stenosis of the duct wall, and could not be repaired. Therefore, the injured bile duct was transected, and a hepatic-jejunal-lateral Roux-Y anastomosis was performed at the healthy part of the left hepatic duct. After this surgery, the patient had a smooth postoperative recovery, and the total bilirubin gradually decreased to normal. The patient was discharged 41 d after operation. No anastomotic stenosis was found at the 6 mo of follow-up.Not all cases are suitable for endo-GIA transection of Glissonean pedicle, especially in cases of intrahepatic bile duct lesions. PHBDI caused by endo-GIA is very difficult to repair due to extensive ischemia, which requires special attention.©The Author(s) 2022. Published by Baishideng Publishing Group Inc. All rights reserved.