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Perivascular epithelioid cell tumor (PEComa) is a rare mesenchymal neoplasm characterized by a unique dual differentiation toward smooth muscle and melanocytic lineages. While PEComas can arise in various gynecologic organs, primary malignant ovarian PEComa is exceptionally rare and shows a wide spectrum of clinical behaviors. We report a case of a rapidly progressive primary ovarian malignant PEComa with an extremely poor prognosis. A 73-year-old woman presented with fever and malaise. A CT scan incidentally revealed a left ovarian tumor, for which she was referred to our department. Tumor markers were within normal limits, but MRI and CT suggested a left ovarian malignancy. A total hysterectomy and bilateral salpingo-oophorectomy were performed. Pathological examination revealed a 9 cm solid mass with necrosis, cytologic atypia, high mitotic activity (14/HPF), and vascular invasion. Immunohistochemistry was positive for both melanocytic markers (MelanA, HMB45) and the myogenic marker desmin, leading to a diagnosis of malignant PEComa. Based on the presence of multiple worrisome features, the tumor was classified as malignant according to established criteria. Despite the absence of distant metastasis at initial imaging and surgery, the patient was offered adjuvant therapy but declined. She developed local recurrence and lung metastasis 72 days after surgery and died 169 days after surgery. This case highlights the clinical significance of a primary ovarian malignant PEComa and the importance of recognizing its potential for rapid and aggressive progression. The finding that multiple pathological risk factors predicted a poor clinical outcome reinforces the need for accurate diagnosis and prompt consideration of systemic therapy, such as mTOR inhibitors, in addition to surgical resection. This report contributes valuable insights into the clinical course of this rare tumor, underscoring the necessity of close follow-up and multidisciplinary management.