Elimination diets have recently become extremely popular among people with autoimmune diseases. A gluten-free diet is indicated in celiac disease (CD), but some studies show its effectiveness in cases of autoimmunity. The aim of this study was to assess whether the use of a gluten-free diet is also effective in patients with chronic autoimmune thyroid disease (cAITD), which is the most common thyroid autoimmune pathology associated with chronic inflammation, over-reactivity of the immune system, auto-destruction of thyrocytes and hypothyroidism. The final analysis of the study included 62 Caucasian women randomized into a control group (CG: n = 31) and an experimental group on a gluten-free diet (GFDG: n = 31), were subject to a 12-month follow-up, during which the concentrations of thyrotropin (TSH), free triiodothyronine (fT3), free thyroxine (fT4), anti-thyroid peroxidase (anti-TPO) and anti-thyroglobulin (anti-TG) antibodies were assessed at baseline and after 3, 6 and 12 months. During the 12-month follow-up between the CG and the GFDG, no differences were found in anti-TPO and anti-TG antibodies, fT3 or fT4 levels, except a significant reduction in TSH levels in the GFDG. Additionally, performed analysis between individual appointments presented no significant differences in changes in the median concentrations of anti-TPO, anti-TG or fT3, but confirmed a significant decrease in TSH and showed accessory an increase in fT4 after 12 months in GFDG. Statistical analyses performed separately for both groups indicated a constant reduction of anti-TG concentrations in the GFDG. In conclusion, a GFD may be administered in cAITD after ruling out celiac disease, but it is necessary to perform more studies to assess if cAITD patients achieve the benefits of following a GFD. Patients with cAITD should be offered proper nutrition education combined with a healthy lifestyle promotion.