Introduction/Objectives: Endometriosis affects 10% of women worldwide. It is noteworthy that this condition is often accompanied by pelvic pain and stress. Endometriosis is a debilitating gynecological condition where tissue similar to the uterine lining grows outside the uterus, often causing significant pain and reproductive issues. We aimed to study the relationship between the intensity of pelvic pain, and stress and inflammatory markers in women with deep endometriosis. Methods: This cross-sectional study analyzed women diagnosed with deep endometriosis through imaging, surgery, and/or biopsy. We assessed pain using the Numerical Rating Scale (NRS). Stress was assessed with the Perceived Stress Scale (PSS-10) questionnaire and the serum cortisol levels. Additionally, we analyzed inflammatory markers, including C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR). Results: Fifty-two women, with an average age of 37.8 ± 6.9 years, participated in this study. Forty-four percent of these participants demonstrated high levels of stress, as indicated by scores above 26 on the PSS-10. Those categorized with “high stress” on the PSS-10 questionnaire exhibited significantly higher pain levels compared to those with “low stress” (p < 0.05). Furthermore, patients experiencing more-severe pelvic pain (pain score > 7) had notably higher serum cortisol levels. Women with intense pelvic pain (scores above 7 on the NRS) had significantly elevated serum cortisol levels (Cohen’s d = 0.72; p = 0.018). Conclusions: A positive association was found between stress levels and the intensity of pelvic pain in women with deep endometriosis, suggesting an interconnection between emotional aspects and biological responses.