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Intramural duodenal hematoma (IDH) in children is a rare complication after esophagogastroduodenoscopy. It is commonly described in patients with additional disorders or risk factors, such as coagulopathy. We present a case of a previously healthy 6-year-old boy with a large obstructing intramural duodenal hematoma and concomitant pancreatitis after an elective esophagogastroduodenoscopy. The patient presented with typical symptoms of an IDH, such as abdominal pain and distension, nausea and vomiting. IDH was diagnosed using ultrasound and magnetic resonance imaging examination. Conservative management with gastric decompression using a nasogastric feeding tube, bowel rest, total parenteral nutrition and analgesia was performed. After three weeks, the patient was discharged from the hospital without any complaints. Interventional management of IDH in pediatric patients with a lack of response to conservative therapy or complicating IDH should be discussed in an interdisciplinary team.