A retrospective cohort study of 844 patients investigated the association between immunohistochemical markers CD56, CD38 and chronic endometritis (CE). The levels of CD56 and CD38 were significantly higher in the CE group than in the non-CE group (P < 0.05). Spearman analysis showed a positive correlation between CD56 and CD138 (r = 0.18), CD38 and CD138 (r = 0.38), and CD56 and CD38 (r = 0.33; P < 0.001 for all). The optimal cut-off values were CD56 ≥ 23.5 cells/HPF and CD38 ≥ 0.5 cells/HPF, at which the incidence of CE was significantly higher (χ² = 15.994 and 129.067; P < 0.001). There were no statistically significant differences in the 12-week continuous pregnancy rate between the high and low CD56 or CD38 groups (P > 0.05). However, at the new CD38 cutoff of ≥ 9.5 cells/HPF, the 12-week continuous pregnancy rate was lower in the high value group (χ² = 5.500; P < 0.05). CD56 and CD38 are associated with CE, with CD38 better predicting pregnancy outcomes.