The current biomarkers for postoperative fertility assessment caused by ovarian endometrioma (OE) are insufficient. The present study hypothesized that the peripheral lymphocyte subpopulation can be used as a candidate biomarker of postoperative infertility in OE. The association of the number of circulating CD4/CD8 T, NK, and γδ T cells with postoperative fertility was assessed in 33 OE patients aged 20 ~ 40 years between June 2018 and January 2019. Concomitantly, 68 healthy female subjects were recruited. The changes in the baseline immune characteristics between the two groups were compared. The data demonstrated significant differences in the ratio of CD4/CD8 T cells and the number of CD56+ NKG2D+ NK cells and γδ T cells between OE patients and control subjects. The patients were followed-up till December 2019 and the number of CD56+ NKG2D+ NK cells in the cases was a significant predictor for postoperative fertility as determined by different COX regression models (crude HR = 0.220, 95% CI = 0.059-0.822; adjusted HR = 0.127, 95% CI = 0.024-0.675). A significant delay to successful pregnancy was noted in OE patients (median time, 173 vs. 99 days, log-rank P = 0.013). The present findings suggested that CD56+ NKG2D+ NK cells are a candidate biomarker of postoperative fertility in OE patients. Larger population studies are warranted.