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Despite solid evidence regarding the association of over-hypothyroidism with polycystic ovary syndrome (PCOS), the relationship between PCOS and subclinical hypothyroidism (SCH) is still a topic of debate. In the present population-based study, we aimed to assess if there is a difference between PCOS and the control group regarding the upper reference limit of thyroid stimulating hormone (TSH). We also aimed to identify the prevalence of SCH in women with PCOS compared to controls. This study was conducted on data collected in the Iranian PCOS prevalence study and the Khuzestan PCOS prevalence study. Participants that met our eligibility criteria were categorized into two groups: PCOS (n = 207) and control (n = 644). Quantile and logistic regression models were used to explore the effect of PCOS status on TSH cut-off values and SCH, respectively. The 95 percentiles of TSH were not significantly different in the PCOS group compared to control ones (6.12 and 6.56 microU/mL, respectively). There was no statistically significant association between PCOS status and SCH (OR adjusted: 1.40; 95%CI: 0.79, 2.50; p = 0.2). The prevalence of SCH and the upper reference limit of TSH were not significantly different in PCOS and controls. Investigation of SCH in women with PCOS might be questionable.