Germ cell tumors in extragonadal sites are uncommon; those arising in the urachus are exceedingly rare and limited to a few anecdotal reports. Herein we document an occurrence of yolk sac tumor in a 9-month-old male who presented with abdominal distension. Laboratory investigation revealed elevated lactate dehydrogenase and α-fetoprotein levels; imaging studies were inconclusive as to tumor type or site of origin. The tumor was resected from the base of the umbilicus and histologic examination revealed neoplastic cells arranged in solid nests or microcystic patterns in a fibromyxoid stroma. Schiller-Duval bodies were conspicuous. Immunohistochemical analysis showed lesional cells reactive to α-fetoprotein, SALL4, placental alkaline phosphatase, Glypican-3 and CD117. No teratomatous or other germ cell elements were identified. These findings supported a diagnosis of pure yolk sac tumor arising from the urachus; the clinical, radiological and pathological findings are discussed.