Gangliocytic paragangliomas are infrequent tumors almost exclusively found in the second portion of the duodenum. An unusual case of a gangliocytic paraganglioma in the third portion of the duodenum with obstructive symptoms is herein reported. A 16-year-old male patient presented with epigastric pain, postprandial plenitude and reflux. A barium swallow failed to demonstrate abnormalities. Endoscopy showed a pedunculated submucosal tumor, originating at the third duodenal portion and causing partial obstruction. Biopsy was not performed due to the risk of bleeding. CT scan demonstrated a polypoid lesion. Through a transmesocolic approach and an anterior duodenotomy, resection of the tumor was performed. No lymph node or other organ affection was found. Histologic examination revealed a gangliocytic paraganglioma. Immunohistochemical examination was performed. Gangliocytic paragangliomas originating in the third or fourth portion of the duodenum, as in the present case, are extremely rare. Characteristic histologic features including epithelioid cells, spindle-shaped cells and ganglion-like cells were met. The majority of cases manifest with a similar benign behavior. Local resection of the tumor is recommended for these cases. An infrequent case of a gangliocytic paraganglioma located in the third portion of the duodenum, with a less common clinical presentation, is herein reported.