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Background/Objectives: The gluten-free diet (GFD) may be anti-inflammatory in treating Hashimoto's thyroiditis (HT), but the studies are inconsistent. To determine the effects of the GFD in non-celiac HT. Methods: We included randomized controlled trials from the following databases: Cochrane Central, Embase, Lilacs, Medline, Scopus, and Web of Science. It was registered at Prospero (no. CRD42024566034). The outcomes assessed included free triiodothyronine (fT3), free tetraiodothyronine (fT4), Thyroid stimulating hormone (TSH), Anti-thyroid Peroxidase (TPO), anti-thyroglobulin (Tg), C-reactive protein (CRP), body weight (BW), body mass index (BMI) and adverse effects. Sensitivity, subgroup, meta-regression, bias risk, and evidence analyses' certainty were also conducted. Results: Only three studies were meta-analyzed, comprising 110 participants. The pooled data revealed the evidence was very uncertain about the effect of GFD compared to the control group on mean differences (MD) of: TSH (MD -0.63 uIU/mL; 95% CI -1.63 to 0.36; p= 0.21), fT3 (MD -0.18 pg/mL; 95% CI -0.50 to 0.14; p= 0.28), fT4(MD -0.33 ng/dL; 95% CI -0.89 to 0.23; p= 0.24), anti-Tg (MD -10.07 IU/mL; 95% CI -17.73 to -2.42; p= 0.010), anti-TPO (MD 76.19 IU/mL; 95% CI 46.86 to 108.51; p< 0.00001), CRP (MD -0.12 IU/mL; 95% CI -0.30 to 0.07), BW (MD -1.46 kg; 95% CI -6.70 to 3.77), BMI (MD -1.80 kg/m2; 95% CI -3.30 to -0.31). The quality of evidence was rated as serious methodological concerns to extremely serious imprecision. Conclusion: The GFD decreased Anti-Tg and increased the Anti-TPO levels, both significantly. There were no significant results on fT3, fT4, and TSH.