The relation between histopathological characteristics of papillary thyroid cancer (PTC) and thyroid functioning in patients of different sex was assessed. Levels of thyroid stimulating hormone (TSH) and thyroid hormones (fT3 and fT4) were measured in 576 patients (468 females and 108 males) with histologically confirmed PTC. Extrathyroid extension (ETE) of PTC, lymphovascular invasion (LVI) and lymph node metastasis (LNM) were assessed in patients of different sex. In addition, age, histological type and Hashimoto’s thyroiditis (HT) were considered. We did not find sex differences in PTC staging. However, females demonstrated smaller tumor size and higher microcarcinoma rate, whereas PTC in men was related to a higher LNM incidence. Coexisting HT was found in 33.3% of the observed patients. HT rate was significantly higher in females than in males and was associated with elevated TSH, though, there was no statistically significant relationship between HT and thyroid hormone levels. Coexisting HT significantly decreased the risk of ETE (OR = 0.67; 95% CI 0.44–1.00; P = 0.05) and LNM (OR = 0.59; 95% CI 0.37–0.94; P = 0.028) among males with PTC. However, there was no significant impact of HT on ETE and LNM in females with PTC. The present study showed sex-related differences in TSH levels and microcarcinoma incidence associated with high rate of coexisting HT in females. Coexisting HT was associated with lower rate of LNM and ETE in males that could reflect a potentially protective role of HT in PTC progression.