A 68-year-old man was diagnosed with Cronkhite-Canada syndrome (CCS). He was treated with drug therapy, mainly using steroids, for 3.5 months without success. The patient was managed with oral nutrition and a proton pump inhibitor (PPI) for transit disturbance caused by edema of the terminal ileum due to polyposis. After sudden exacerbation of right-sided abdominal pain, emergency surgery was performed with a diagnosis of upper gastrointestinal perforation. In addition to filling the perforated portion of the anterior wall of the duodenal bulb with the great omentum, the ileum was resected and ileostomy was performed. Postoperatively, CCS symptoms were improved by administration of steroids and anti-TNF-alpha antibody, and the PPI was changed from intravenous to oral immediately after surgery, with no recurrence of duodenal ulcer. This case suggests that surgical resection of the main lesion only should be considered for patients with intractable CCS.