Cases of neonatal gastrointestinal system(GIS) obstruction are quite complex for pediatric surgery clinics. A rare cause of intestinal obstruction is the duplication cyst (DC). Athree-day-oldmale patient presented at our clinic with a history of abdominal distension and bilious vomiting on the second day following birth. Although pathology had not yet been determined from observation and examination, surgery was performed when the patient could not tolerate oral feeding. An ileal DC forming an incomplete obstruction was observed. Ileoileal anastomosis was performed on the patient. Because DCs can present with different clinical symptoms, it is quite difficult to diagnose them in neonate patients. Lacking an imagingmethod that can provide an exact diagnosis, the diagnostic laparotomy is a suitable approach for both diagnosis and treatment to avoid delays in treatment.