The Fc receptor-like 3 (FCRL3) gene was reported to be linked to a variety of autoimmune diseases, including endometriosis-related infertility. However, this linkage has not been studied in Chinese population and there has been no meta-analysis on the interrelationship of FCRL3 gene and endometriosis-related infertility. The aim of the study was to investigate the association between FCRL3 genetic polymorphisms and the risk of endometriosis-related infertility in Han Chinese, and a further meta-analysis was conducted to confirm our results.Four single nucleotide polymorphisms (SNPs) (rs7528684 [FCRL3_3], rs11264799 [FCRL3_4], rs945635 [FCRL3_5], and rs3761959 [FCRL3_6]) on FCRL3 gene were genotyped in a case–control cohort composed of 217 patients suffering from endometriosis-related infertility and 220 healthy controls using cleaved amplification polymorphism sequence-tagged sites (polymerase chain reaction–restriction fragment length polymorphism, PCR–RFLP). Odds ratio (OR) and its 95% confidence interval (CI) was used to evaluate the association quantitatively. Furthermore, a meta-analysis of previous studies including the present study was implemented through Stata 11.0 (Stata Corporation, College Station, TX).We found an approximately 1.4-fold significantly increased frequency of the FCRL3_3 variant in women with endometriosis-related infertility over the controls (OR = 1.41 [95% CI = 1.08–1.84], P = 0.013). However, no significant difference was found between women with endometriosis-related infertility and controls for FCRL3_4, FCRL3_5, and FCRL3_6. Regardless of the symptoms and the revised classification of the American Society of Reproductive Medicine (rASRM) stage of endometriosis, there was a significant association between FCRL3_3 variant and an increased risk of endometriosis-related infertility. Meta-analysis of previous studies combined with the present study further confirmed the association between FCRL3_3 and the risk of endometriosis-related infertility.In summary, the present study suggested that FCRL3_3 variant was associated with an increased risk of endometriosis-related infertility, regardless of symptoms, and rASRM stage of the patients. Meta-analysis of previous studies combined with the present study further confirmed our results. Further large-scale studies in the future are warranted to explore the association between FCRL3 genetic polymorphisms and endometriosis-related infertility, as well as other human diseases, in Asian and other ethnicities.