Background: Evidence suggests that selenium supplementation could be useful in the treatment of Hashimoto thyroiditis (HT), but the available trials are heterogeneous. This study investigates clinically relevant effects of selenium supplementation in patients with HT.Methods: A systematic search was performed in PubMed, Web of Science, EMBASE, Scopus, and the Cochrane Library. The latest update was performed on December 3, 2022. We investigated the changes in thyroid peroxidase antibodies (TPOAb) and thyroglobulin antibodies (TgAb) after selenium supplementation. The effect sizes were expressed as weighted mean difference (WMD) with 95% confidence intervals (CIs).Results: After screening and full-text assessment, 7 controlled trials comprising 342 patients were included in the systematic review. The results showed that there was no significant change in TPOAb levels (WMD = −124.28 [95% CI: −631.08 to 382.52], P = .631, I 2 = 94.5%) after 3 months of treatment. But there was a significant decrease in TPOAb levels (WMD = −284.00 [95% CI: −553.41 to −14.60], P < .05, I 2 = 93.9%) and TgAb levels (WMD = −159.86 [95% CI: −293.48 to −26.24], P < .05, I 2 = 85.3%) after 6 months of treatment.Conclusions: Selenium supplementation reduces serum TPOAb and TgAb levels after 6 months of treatment in patients with HT, but future studies are warranted to evaluate health-related quality or disease progression.