Aims: To determine the effects of a tumor necrosis factor inhibitor (etanercept) on pregnancy outcomes in patients with endometrioma who were treated with assisted reproductive technology. Methods: Sixty-eight infertile patients who had endometrioma were included in our retrospective case-control study. We administered etanercept (Enbrel, 50 mg in 1 mL intramuscularly) to 19 patients on the second day of their previous menstrual cycle. All patients were treated with assisted reproductive technology. Pregnancy and live birth rates (LBR) were documented. Results: When all other parameters (age, body mass index, infertility) are supposed to be constant, the clinical pregnancy rate was significantly higher in patients who used etanercept in an antagonist protocol than in patients who did not use etanercept (χ2 = 5.547; p = 0.019) but LBR did not reach a statistical significance (χ2 = 3.179; p = 0.075). The use of etanercept had an OR of 4.17 (95% CI 1.23–14.14) compared with not using etanercept for clinical pregnancy rate. The use of etanercept increased the rate of pregnancy (χ2 = 6.55; p = 0.01). The pregnancy rate with the use of etanercept had an OR of 4.23 (95% CI 1.35–13.25) compared with patients who did not use etanercept. In the same way, the use of etanercept increased LBR twofold, but it is not significant in the border line (χ2 = 3.771; p = 0.052). Conclusions: Etanercept may be a new non-hormonal therapy that may be an adjunct to treatment of infertile women with endometrioma. However, the safety of etanercept on embryos and fetuses has not been fully clarified.