Abstract Background Pneumothorax during surgery under general anesthesia is a life-threatening situation for the patient because it can progress easily to the tension pneumothorax due to positive pressure ventilation unless appropriate treatments such as inserting a drainage tube in the thoracic cavity are initiated. The authors experienced a case of intraoperative pneumothorax and the diffuse dissection of visceral pleura during liver transplantation surgery, and achieved successful repair by a trans-diaphragmatic approach without changing patient’s body position. Case presentation A 66-year-old male with multiple liver and renal cysts caused by autosomal dominant polycystic kidney disease (ADPKD) was admitted to the authors’ hospital for treating the infection of the liver cysts. The infection was unable to be controlled by conservative treatments. Therefore, the patient was planned to undergo living-donor liver transplantation. Intraoperatively, the liver was found to swell markedly and to firmly adhere to the right diaphragm. After the extraction of the liver, because the right diaphragm swelled markedly, pneumothorax was suspected. Chest tube was inserted immediately, and the small incision was made in the right diaphragm. Thoracoscopic observation revealed that (1) the visceral pleura of the bottom of the right lung widely expanded like a giant cyst due to the dissection from the lung parenchyma and (2) a large air leakage from a pin hole appeared in the dissected pleura. After the completion of the liver transplantation, the thoracoscopic leakage-closing operation was performed through the right diaphragm incision. Because the dissection of visceral pleura was too wide to perform plication or cystectomy by a stapler or sutures, the dissected pleura was opened, and absorbable fibrin sealant patches and fibrin glue were put or injected between the lung parenchyma and the pleura. Although, after being observed postoperatively, prolonged minor air leakage disappeared by a conservative drainage treatment, and the cyst on the bottom of the right lung disappeared on chest computed tomography (CT). Conclusions Although intraoperative pneumothorax and broad dissection of visceral pleura during laparotomy is a complicated situation, the authors successfully repaired air leakage via a trans-diaphragmatic approach without changing the patient’s body position.