While infections have been implicated in endometriosis pathogenesis, the role of human papillomavirus (HPV) remains unclear. This study combined a meta-analysis of seven studies with a case-control study (n = 432 surgically treated patients) to evaluate the association of HPV infection with endometriosis risk and fertility outcomes. The meta-analysis showed no significant association between HPV infection and endometriosis risk, either for any HPV subtype (pooled odds ratio [OR] = 2.60, 95% confidence interval [CI]: 0.28–23.87) or high-risk subtypes (OR = 1.68, 95% CI: 0.49–5.75). Notably, HPV prevalence was higher in patients with endometriosis (46% overall; 36% for high-risk subtypes) than in the general population. Evidence regarding the association between HPV infection and fertility outcomes remains limited, with only two eligible studies identified. Our case-control analysis revealed that HPV-positive patients had significantly reduced postoperative live birth rates compared with HPV-negative counterparts (10.6% vs. 21.0%, P < 0.05). These findings suggest that HPV infection is unlikely to be a major risk factor for endometriosis development, but it may be associated with poorer postsurgical fertility outcomes. The dual-method approach strengthens the evidence for HPV's clinical impact on reproductive prognosis in patients with existing endometriosis.