Background <p>Radiotherapy (RT) plays a key role in multidisciplinary treatment of Head and neck cancers (HNCs). Over the past two decades, advances have improved RT’s tumor control and toxicity profiles. Precise delineation of gross tumor volume and organs at risk using CT and PET-CT is crucial for safe and effective RT. Additionally, RT increases the risk of thyroid dysfunction, especially hypothyroidism.</p> Aim <p>The present study compared PET-CT simulation and CT-alone planning in head and neck cancer (HNC) treatment, emphasizing their effects on thyroid gland function.</p> Methods <p>The patients were divided into two groups according to the simulation method (PET-CT or CT), two fresh blood samples (5 mL/ sample) were collected from each patient, before and after radiotherapy. TSH, FT3, and FT4 (Thyroid biomarkers) were assessed by electrochemiluminescent immunoassay (ECLIA).</p> Results <p>PET-CT simulation demonstrated a significant improvement in GTVp delineation accuracy by 71.8% compared with CT. After radiotherapy, TSH levels show minor decline changes, whereas FT3 and FT4 levels declined significantly, with greater declines observed in stages II and III. The most common tumor site was the larynx (60% in PET-CT, 75% in CT), followed by the tongue, nasopharynx, and parotid gland.</p> Conclusion <p>PET-CT simulation offered superior GTVp delineation accuracy over CT, improving HNCs radiotherapy planning. Immediately after RT, radiotherapy caused significant declines in serum FT3 and FT4 levels, with only a minor, non-significant TSH declining, particularly in stage II/III disease. Notably FT4 is little more affected in PET-CT simulation patient group, highlighting the need for thyroid function monitoring. These results advocate PET-CT integration in planning and routine endocrine monitoring for treatment complications.</p>