Background: Portal venous gas (PVG) and pneumatosis intestinalis (PI) are rare pathologic findings, and a delayed appearance of portal vein thrombosis (PVT) in such patients is extremely rare. Case Presentation: A 51-year-old man complaining of epigastric pain was referred to our hospital. Computed tomography (CT) at admission revealed massive PVG and extensive PI, but no PVT. Emergency laparotomy was carried out, but bowel resection was unnecessary. On follow-up CT on postoperative day 5, thrombosis was noted in the portal venous system, and anticoagulant was started immediately. This patient was discharged and continued to take the anticoagulant. Seven months after discharge, PVT had disappeared on CT without any thromboembolic complications. Conclusion: If acute PVT is detected, anticoagulant is needed to prevent bowel ischemia and/or portal hypertension due to the growth of the thrombus. Clinicians should be aware of the potential for such a complication, and make their best efforts to exclude this entity using CT or sonography.