Thyroid cancer is one of the most malignant tumors and a serious threat to human health. Selenium (Se) is an essential trace element that is critical for thyroid function. Since the relationship between Se and thyroid cancer remains unclear, a meta-analysis was performed to clarify the relationship. A total of five databases (PubMed, Web of Science, Scopus, Embase and Cochrane library) were searched for case-control studies and cohort studies on serum levels of Se and thyroid cancer published up to 13 July 2022. Seven articles consisting of 10 case-control studies and comprised of 2,205 subjects met the inclusion criteria for meta-analysis. From the 10 selected studies, pooled analysis indicated that thyroid cancer patients had lower serum levels of Se than healthy controls [standardized mean difference = -1.25, 95% confidence interval = (-2.07, -0.44), P = 0.003]. Our meta-analysis supports a significant relationship between serum levels of Se and thyroid cancer.