Background: Perforation of a duodenal diverticulum is a rare complication that may become fatal with a delay in appropriate treatment. However, the optimal treatment for perforated duodenal diverticulum remains controversial, ranging from conservative therapy to surgery including pancreatoduodenectomy. Case presentation: The patient was a 60-year-old woman with no particular medical history who visited our hospital with chief complaints of continuous fever and right dorsal pain. Upon arrival, she had tenderness in the right upper quadrant of the abdomen. Laboratory data showed the elevation of inflammatory markers. Computed tomography revealed free air with abscess formation around the duodenum, which was diagnosed as duodenal perforation with abdominal abscess. We decided on emergent surgery, and we identified the perforation site on the dorsal side of the second portion of the duodenum intraoperatively. However, the inflammation around the perforation site was severe, and it was difficult to perform primary closure or dissection of the perforated diverticulum. Therefore, we finished surgery by placing four indwelling intra-abdominal tubes. Since postoperative day (POD) 1, the elevation of inflammation markers appeared to be uncontrollable, owing to the leakage of bile and pancreatic juice. We decided to perform endoscopic retrograde cholangiopancreatography on POD 2, and inserted endoscopic nasobiliary drainage and nasopancreatic drainage tubes. The patient showed a good postoperative course and was discharged on POD 57. Conclusions: Endoscopic nasobiliary and nasopancreatic drainage in combination with surgical drainage may be an effective treatment for perforated duodenal diverticulum.