Thyroglossal duct cysts (TDC) are the most common cervical cysts and are usually considered to be a benign embryonic malformation where the thyroglossal duct fails to obliterate. Parathyroid cysts (PTC) are a rare disease and may also result from malformation of the remnants of the third pharyngeal pouch. Although several sporadic cases of concurrent TDC with other head and neck malformations have been reported in the literature, a combination of TDC and PTC has never been reported. Here, we report the first case of a 35-year-old woman with a metachronous TDC and PTC. The embryologic origins of TDCs and inferior PTCs are revealed from the experience of this case.