Yolk sac tumors are highly malignant and commonly affect the ovaries, with a median age of occurrence of 23 years. We describe the case of an ovarian yolk sac tumor in a 12-year-old premenarchal girl suffering from Hashimoto’s thyroiditis and chronic spontaneous urticaria, which presented as a rapidly growing solid cystic formation in the hypogastrium with an extreme increase in alpha fetoprotein (52,778 mg/ml). After ultrasound and MRI imaging, fertility-sparing staging surgery was performed, and the diagnosis of an ovarian yolk sac tumor with positive malignant cells in ascites was confirmed. The specificity of this case is the tumor classification into stage IC3 according to the FIGO and stage III according to the Children’s Oncology Group criteria. The postoperative course was complicated by a pelvic abscess and a subcutaneous suture rejection reaction. Our case may incite further research on the relationship between autoimmunity and yolk sac tumors.