Hashimoto’s disease (HD) is one of the major clinical subtypes of autoimmune thyroid disease. Both environmental and genetic factors contribute to the pathogenesis of HD. Previous evidence has shown that both IRAK2 and TLR10 are potential candidate susceptibility genes for HD. In this study, a total of 3654 Chinese women, including 973 HD cases and 2681 healthy controls, were recruited. Thirty-three tag single nucleotide polymorphisms (SNPs) in IRAK2 and TLR10 were genotyped. Genetic association analyses at both the single-marker and haplotype levels were performed. Gene-by-gene interaction analyses were also conducted in case-only samples, as well as eQTL analyses for significant SNPs based on data extracted from the GTEx database. We identified that two SNPs, rs165501 (OR = 1.20, P = 0.0008, IRAK2) and rs10004195 (OR = 1.23, P = 0.0001, TLR10), were identified to be significantly associated with HD. Rs10004195 was significantly associated with the gene expression of TLR10 in human pituitary tissues (P = 2.00 × 10−4), while rs165501 was significantly associated with the expression of IRAK2 in human thyroid tissues (P = 3.10 × 10−6). No significant results were obtained in the gene-by-gene interaction analyses. Our findings suggest that both IRAK2 and TLR10 play important roles in the onset and development of HD.