Only a few reports of thyroid gland paragangliomas are presented in the world literature. We present a clinical case of a rare intrathyroid neck paraganglioma in a 49-year-old male who presented with a nodular mass of the right thyroid gland. Cytological examination showed a pattern similar to C-cell carcinoma, but basal calcitonin levels remained within the reference interval (7 pg/mL). The patient underwent thyroidectomy with central lymph node dissection, and paraganglioma was suspected based on pathomorphological examination. Immunohistochemical examination showed expression of SSTR2 (+++), SSTR5 (+), synaptophysin, chromogranin A, vimentin, and S100 and a lack of expression of calcitonin and broad-spectrum cytokeratins. Additional genomic sequencing revealed a heterozygous mutation in the SDHD gene (HG38, chr11:112089002A>G, c.305A>G). The set of diagnostic tests helped to diagnose and determine the further strategy of patient management accurately.