Introduction: Struma ovarii accounts for 2% of mature teratomas. Struma ovarii is diagnosed when thyroid tissue accounts for >50% of the teratoma. Malignant transformation is rare, occurring in <5% of struma ovarii cases. Case presentation: A 17-year-old patient was diagnosed with papillary thyroid cancer in struma ovarii. The patient exhibited menstrual disorders. Abdominal and pelvic CT revealed a 17 cm mass in the left adnexa. Laparoscopic removal of the left adnexa with enucleation of right ovarian cysts was performed. Histopathological diagnosis was a follicular variant papillary carcinoma measuring 23 mm in diameter. Immunohistochemical positive expression of CK19, TTF-1, and thyroglobulin (Tg) confirmed the diagnosis. Molecular analysis detected the mutation in ovarian tumor tissues. Preoperative serum Tg concentration was >300 ng/mL, which decreased to 38.2 ng/mL after gynecological surgery with undetectable anti-Tg antibodies. The patient underwent total thyroidectomy with no cancer detected on histopathological examination. The patient was treated with I-131 and showed no recurrence 4 years after the diagnosis. Conclusions: Malignant struma ovarii is diagnosed by surgery. Because papillary carcinoma in struma ovarii is rare and there are no guidelines regarding the management of this type of cancer, therapeutic decisions should be made individually based on clinical and pathological data.