Congenital diaphragmatic hernia (CDH) is a birth defect of the diaphragm resulting in pulmonary sequelae that threaten the lives of infants. In computed tomography (CT) images of a 17th century middle-aged male mummy (the Andong mummy), we observed that the abdominal contents had protruded into the right thoracic cavity through the diaphragmatic defect, accompanied by a mediastinal shift to the left. On autopsy, the defect in the right posterolateral aspect of the diaphragm was reconfirmed, as was the herniation of the abdominal organs. The herniated contents included the right lobe of the liver, the pyloric part of the stomach, a part of the greater omentum, and the right colic flexure connecting the superior part of the ascending colon and the right part of the transverse colon. Taking our CT and autopsy results together, this case was diagnosed as the Bochdalek-type CDH. Herein we make the first ever report of a CT-assisted diagnosis of a pre-modern historical case of CDH. Our results show the promising utility of this modality in investigations of mummified human remains archaeologically obtained.