Paraganglioma of the thyroid is a neuroendocrine tumor originating from the neural crest. To our knowledge, only 32 cases of thyroid paraganglioma(TP) have been reported to date. TP is difficult to distinguish from medullary thyroid cancer(MTC), hence correct diagnosis is seldom obtained preoperatively. Although immunohistochemistry is helpful for confirmation of TP, these markers are not specific for differential diagnosis between TP and MTC. Therefore, an index of suspicion is important when encountered with MTC with unusual features, or given pathology with neuroendocrine features and unusual immunohistochemical findings. The authors report a case of TP misdiagnosed as MTC at preoperative work-up and intraoperative frozen section analysis, with a review of the literature. The case depicts various immunohistochemical characteristics of the tumor.