Primary squamous cell carcinoma of the thyroid gland (PSCCTh) and anaplastic thyroid carcinoma with extensive squamous differentiation are rare entities which pose a diagnostic challenge in determining the primary site when presented as metastases. The difficulty in confirming a thyroid primary is further compounded by the aggressive nature of these tumours which frequently present at advanced stages. We present a case in which the patient presented with a thyroid mass and a lung mass simultaneously. The risk of misinterpreting the site of primary tumour as lung is greatly increased because squamous cell carcinoma of lung is much more common than its thyroid counterpart. This case highlights the effectiveness of PAX-8 stain in determining the primary site of tumour when squamous cell carcinoma is found in both lung and thyroid gland.