Background/Objectives: The prognosis of endometriosis-related ovarian clear cell carcinoma (OCCC) versus non-endometriosis-associated OCCC remains unclear. We examined the impact of endometriosis on OCCC diagnosis and progression and assessed whether prior surgical intervention for endometriotic ovarian cysts affects prognosis. Methods: In this retrospective study (2006-2024), OCCC patients were classified as non-endometriosis-associated or endometriosis-related. A subgroup analysis compared endometriosis-related OCCC patients with and without a history of endometriotic ovarian cyst surgery. Results: The average CA-125 level was 104.20 (29.90, 347.70) in the non-endometriosis-associated OCCC group and 80.70 (32.40, 247.90) in the endometriosis-related OCCC group (p = 0.32). Early-stage diagnosis occurred in 62.77% and 75.21% of these groups, respectively (p = 0.046). The average age at diagnosis was 53.95 ± 9.71 years for the non-endometriosis-associated group and 45.68 ± 7.98 years for the endometriosis-related group (p < 0.001). Mortality or poor prognosis was observed in 24.11% and 17.80% of these groups, respectively (p = 0.226). In endometriosis-related OCCC, comparisons were made between patients with and without a history of endometriotic ovarian cyst surgery. The average age at diagnosis was 45.84 ± 8.24 years for those without a surgical history and 44.71 ± 6.35 years for those with a surgical history (p = 0.59). Early-stage diagnosis was observed in 77.23% and 62.50%, respectively (p = 0.339). Mortality or poor prognosis occurred in 14.85% of those without a surgical history and 35.29% of those with a surgical history (p = 0.008). The hazard ratio for women with a surgical history was 3.48 (1.29-8.69) (p = 0.008). The incidence rate was 3.17 per 1000 person-years (PYRs) for individuals without surgery and 13.36 per 1000 PYRs for those with a history of surgical intervention (p = 0.008). Conclusions: Endometriosis did not impact the prognosis of women with OCCC. However, women with endometriosis-related OCCC were diagnosed at earlier stages and at younger ages. A history of endometriotic ovarian cyst surgery did not influence OCCC detection but was linked to poorer survival outcomes.