Abstract Background Small intestine duplication cysts (SIDCs) are rare congenital anatomical abnormalities of the digestive tract and a rare cause of hematochezia. Case presentation We describe an adult female presented with recurrent hematochezia. The routine gastric endoscope and colonic endoscope showed no positive findings. Abdominal CT scan indicated intussusception due to the "doughnut" sign, but the patient had no typical symptoms. Two subsequent capsule endoscopes revealed a protruding lesion with bleeding in the distal ileum. Surgical resection was performed and revealed a case of SIDC measuring 6 * 2 cm located inside the ileum cavity. The patient remained symptom-free throughout a 7-year follow-up period. Conclusion SIDCs located inside the enteric cavity can easily be misdiagnosed as intussusception by routine radiologic examinations.