Background: Endometriosis is one of the common benign gynecological diseases among reproductive aged women, which almost lead to pelvic pain, infertility and menstrual disorders. There is no blood test available for the diagnosis of endometriosis. MUC17 has been revealed to play a role in a variety of cancers, but the role of MUC17 single nucleotide polymorphisms (SNPs) in endometriosis susceptibility remains unclear. Methods: In the present study, genotyping for four MUC17 polymorphisms in 117 endometriosis patients and 118 female control participants was undertaken using the Agena Mass ARRAY. An unconditional logistic regression model was used to estimate the role of MUC17 gene polymorphisms in endometriosis. Results: Bioinformatics analysis showed that rs6966570 could be relevant to the transcription factor binding sites of proteins bound and was related to expression quantitative trait Loci (eQTL) and Motifs. Rs10246021 affected eQTL and Motifs. Nevertheless, there was no significant difference in the frequency of mutation of MUC17 gene between the case group and the control group (p > 0.05), the C allele of rs11979706 (OR: 0.37; 95% CI: 0.18–0.74; p: 0.03), the T allele of rs10246021 (OR: 0.43; 95% CI: 0.21–0.88; p: 0.018), the T allele of rs6966570 (OR: 0.45; 95% CI: 0.22–0.92; p: 0.026), and the T allele of rs4729655 (OR: 0.48; 95% CI: 0.26–0.88; p: 0.017) may be protective factors for the occurrence of dysmenorrhea in endometriosis. Logistic regression analysis indicated genotypes MUC17 rs11979706 CC and rs4729655 TT contribute a lower risk to dysmenorrhea (p = 0.024, p = 0.034), respectively. Haplotype analysis showed that individuals with CTTT haplotypes had a lower risk of developing dysmenorrhea (p = 0.008). In the log-additive model, the rs4729655 was associated with endometriosis-induced infertility. Conclusions: On the whole, these findings demonstrate that MUC17 gene polymorphisms was not correlated with endometriosis susceptibility but was associated with secondary dysmenorrheal and infertility in Central Plains Chinese women.