We describe a case of primary malignant paraganglioma of the thyroid gland that was found in a 55-year-old woman who had undergone surgery for bilateral carotid body tumors. The paraganglioma was treated with a total thyroidectomy followed by radiation therapy, and the patient was disease-free after more than 2 years of follow-up. Malignant paragangliomas of the thyroid gland are extremely rare. The diagnosis of malignancy is based on histopathologic findings, tumor behavior, and metastasis. These tumors can be misdiagnosed as other types of thyroid malignancies, thus resulting in less than optimal treatment. A genetic etiology was suspected in our patient.