A man in his 40s visited our hospital with a chief complaint of upper abdominal pain after defecation. His general and local conditions were good. Intraperitoneal free air was detected on an abdominal computed tomography (CT) scan, and laboratory tests revealed leukocytosis. Esophagogastroduodenoscopy showed no abnormalities. Emergent laparotomy was performed because of the suspected intestinal perforation, but neither perforation nor peritonitis was observed. Bacterial culture of intraperitoneal lavage fluid was negative. The postoperative course was uneventful and he was discharged. Because the cause of pneumoperitoneum was unknown, the diagnosis was idiopathic pneumoperitoneum. However, we had the opportunity to evaluate abdominal CT images taken with the lung window setting 4 years before the operation, which showed pneumatosis intestinalis in the ileocecal region. It has been reported that metachronous pneumatosis intestinalis is sometimes detected in cases of pneumoperitoneum with pneumatosis intestinalis. Thus, pneumatosis intestinalis was suspected as the cause of pneumoperitoneum in this case.