Background: Thyroid autoimmunity is an immune response to thyroid antigens that causes varying degrees of thyroid dysfunction. The sole effective treatment for Celiac Disease (CD) is a gluten-free diet (GFD). However, the association between GFD and thyroid autoimmunity in patients with CD has not been confirmed. Methods: A comprehensive search of several databases, involving PubMed, Embase, Web of Science, Medline, and Cochrane databases, was conducted to identify studies that primarily addressed the effects of GFD on thyroid autoimmunity in CD subjects. The meta-analysis involved studies that compared the risk of ATPO and ATG antibody positivity in CD patients with GFD, the risk of developing AITD, and the risk of developing thyroid dysfunction. Fixed-effects models or random-effects models were used to calculate the odds ratios (ORs) and their 95% confidence intervals (95% CIs). Results: A total of 10 observational studies met the inclusion criteria and included 6423 subjects. The results indicated that GFD is positively associated with thyroid autoimmunity in the children subgroup of CD patients (OR = 1.61, 95%CI 1.06-2.43, P = 0.02). However, there was no significant difference in thyroid autoimmunity between the group adhering to GFD and the control group in the total CD population. Conclusion: The results seem to indicate that subjects with a more pronounced autoimmunity (such as to have an early onset of CD) appear to have a greater risk of thyroid autoimmunity.