Background Polycystic ovary syndrome (PCOS) and hypothyroidism are the most common endocrinological disorders among women of reproductive age. Since hypothyroidism occurs more frequently in PCOS patients, it is vital to explain its clinical impact. Aim To evaluate the impact of subclinical hypothyroidism (SCH) and its treatment on the metabolic profile of patients with PCOS. Methods 190 women with PCOS phenotype A were enrolled in the case-control study. They were divided into three groups: 38 women with PCOS and subclinical hypothyroidism, 76 women with PCOS and SCH under thyroid replacement therapy, and 76 women with PCOS and normal thyroid function (control group). Serum lipids, fasting glucose, and insulin, as well as oral glucose tolerance tests were performed. Results In the analyzed parameters, there were no statistic differences between the groups in relation to thyroid function. BMI turned out to be the main factor dividing the patients in terms of serum lipids, fasting glucose, fasting insulin, and oral glucose tolerance test. TSH was associated with total cholesterol and LDL cholesterol levels, whereas BMI has a dominant impact on HDL cholesterol, triglycerides, glucose, and insulin resistance. Conclusions SCH is associated with mild lipid serum alterations in women with PCOS, but it is BMI to have a dominant impact on glucose and insulin. It seems that treatment of SCH in PCOS does not significantly alter lipid and glucose metabolism.