Studies have been conducted with the purpose of elucidating thyroid gland dysfunction in obesity, however the contributing factors for such dysfunction are not yet fully understood. Selenium is notable for its role in thyrocyte protection against oxidative damage and control of thyroid hormone synthesis. In addition, subjects with obesity may exhibit alterations in the selenium homeostasis. Therefore, the present study aimed to examine the selenium status and its relationship with serum thyroid hormone levels in obese women. This cross-sectional study included 69 euthyroid women, aged between 18 and 50 years, who were divided in two groups: an obese group (n = 35) and a control group with women of normal weight (n = 34). Selenium intake was assessed by three-day diet records and analyzed using NutWin software version 1.5. Plasma, erythrocyte, and urinary selenium levels were determined using inductively coupled plasma optical emission spectrometry. Testing for thyroid hormones and thyroid autoantibodies was performed based on chemiluminescence. The median dietary selenium content was adequate according to the recommendations, with no statistical difference between groups. Obese women had reduced plasma and erythrocyte selenium levels compared to the control group, although selenium concentration in erythrocytes was adequate within the normal range for both groups. There was no significant difference between the urinary selenium concentrations in the subjects; however, the mineral clearance was higher in the obese group. Free triiodothyronine (fT3) and free thyroxine (fT4) levels were higher in obese women with class II obesity when compared to the control group. There was a negative correlation between plasma selenium and serum fT4 levels. Obese women showed impairment in selenium homeostasis, however, this fact did not seem to adversely affect thyroid metabolism.