Yolk sac tumors, a subset of malignant germ cell tumors originating from gonadal germ cells, most often present as ovarian or testicular tumors in adolescents, sometimes in combination with different histologies as a mixed malignant germ cell tumor. We describe a toddler presenting with severe iron deficiency anemia who was found to have a gastric pure yolk sac tumor. She underwent a partial gastrectomy and received adjuvant systemic chemotherapy. This is the first reported case of a gastric pure yolk sac tumor in a child, brought to clinical attention due to significant gastrointestinal blood losses.