The prevalence of genital human papillomavirus (HPV) in women with endometriosis has never been reported in a national representative survey. We aimed to investigate the association of endometriosis with the prevalence of HPV. We analyzed the data on 1768 women (representing 43,824,157 women) in the United States aged 20–54 years from the National Health and Nutrition Examination Survey in the prevaccination era (2003–2006). The diagnosis of endometriosis was based on a self-report. The prevalence of any HPV in women with endometriosis did not differ from that in women without endometriosis after controlling for potential confounders such as age, ethnicity, family income, marital status, and the number of deliveries (adjusted prevalence ratio (aPR) 0.84, 95% confidence interval (CI) 0.61–1.15). No significant association was found between the prevalence of high-risk HPV and the diagnosis of endometriosis (aPR 0.71, 95% CI 0.44–1.14). If the participants were not covered by health insurance, the prevalence of any HPV infection in women with endometriosis was higher than in those without endometriosis (aPR 1.44, 95% CI 0.94–2.20). In contrast, in a subgroup who had health insurance, a lower prevalence of any HPV infection was observed in women with endometriosis (aPR 0.71, 95% CI 0.50–1.03), and P for interaction was statistically significant (P = 0.01). There was no association between endometriosis and HPV infection in this study of HPV vaccine-naïve women of reproductive age. The association was not different by the type of HPV. However, access to healthcare may modify the association between endometriosis and HPV infection.