A 35-year-old woman presented to her primary care physician with early satiety, weight loss, nausea, vomiting, and pruritus. She was eventually found to have a pancreatic mass obstructing the bile duct. The mass was evaluated by endoscopic retrograde cholangiopancreatography (ERCP) and endoscopic ultrasonography (EUS) with biopsy. Histopathology results revealed a high grade malignant neoplasm of uncertain type. The tumor was further characterized by open biopsy, which revealed a yolk sac tumor (endodermal sinus tumor). Her disease was unresectable. Serum alpha-fetoprotein (AFP) levels were markedly elevated (693.3 ng/ml; reference range: 0-8 ng/ml). The patient was treated with bleomycin, etoposide, and cisplatin (BEP) with a partial response and a persistently elevated serum AFP of 139.7 ng/ml. She then received salvage chemotherapy with paclitaxel, ifosfamide, and cisplatin (TIP), with a minimal response (serum AFP, 68 ng/ml). She next received an autologous bone marrow transplant, with a decline in AFP to 19 ng/ml after the first of two tandem transplants. This case report illustrates a rare presentation of an extragonadal endodermal sinus tumor in a woman with biliary tract obstruction as the predominant manifestation.