Background: Internal herniation through lesser omentum hiatus and gastrocolic ligament with malrotation is extremely rare. This type of internal hernia has rarely been described before. Preoperative diagnosis is difficult and prone to misdiagnosis. Case presentation: A 38-year-old Chinese woman was an emergency admission to our hospital with a sudden onset of acute epigastralgia for the past 14 hours. We made a presumptive diagnosis of gastrointestinal perforation and septic shock. Due to the acute onset and rapid progress, she received timely surgical treatment. During operation, we observed that her small intestine herniated into the hepatogastric ligament and ligamentum gastrocolicum hiatus accompanied with intestinal malrotation that resulted in internal hernia. We found a diverticulum of approximately 3.0 × 6.0 cm sited at a distance of 80 cm from the ileocecal intestine. We resected the strangulated intestinal loop and the diverticulum, performed an appendicectomy, and closed the ligamentous fissure. Postoperation, she recovered smoothly, without any complications, and was discharged on day 6. Conclusions: A case of internal hernia formation is quite rare; accurate preoperative diagnosis and timely surgery are essential because it can cause strangulation of the ileus. However, the incidence of this internal herniation is low and preoperative diagnosis is difficult. An accurate preoperative diagnosis of internal hernia is still a challenge. © 2017 The Author(s).