The impact of selenium on the course of Hashimoto’s thyroiditis (HT) was mainly assessed by monitoring the titer of antithyroid autoantibodies in most of the studies conducted hitherto. On the other hand, the imbalance in activity of T cells such as Th1, Th2, Th17, and Treg may be relevant in the pathogenesis of this disease. Hence, the assessment of changes in the secretion of cytokines by these cells during selenium supplementation in patients with HT seems to be an important issue and was the main goal of this study. A further aim was to search for correlations among these cytokines, as well as markers of thyroid function, selenium/iodine status in the body, and other biochemical parameters. The group of 29 women with newly diagnosed Hashimoto’s thyroiditis was supplemented with selenium in a dose of 100 µg/day for 6 months. Immunological parameters: interferon γ, tumor necrosis factor α, chemokine CXCL10, interleukin 4, interleukin 1β, interleukin 17, transforming growth factor β, and C-reactive protein, as well as selenium status parameters were determined in serum twice, i.e., before and after supplementation. Selenium supplementation was associated with a change in the production of two cytokines: interferon γ and interleukin 1β, for which a decrease and an increase in concentration were observed, respectively. The partial least squares (PLS) model revealed the presence of many relevant correlations among analyzed parameters. The stage of HT development, degree of thyroid dysfunction, and selenium supplementation of diet are interdependent factors which shape the profile of some cytokines secreted by cells participating in the autoimmunity process.