Objective: To investigate whether systemic lupus erythematosus (SLE) has a negative impact on the fertility of young women of reproductive age through SLE activity and therapy. Methods: This retrospective case–control study was conducted in 50 patients with SLE and 50 healthy controls who fulfilled the 1997 American College of Rheumatology criteria. Anti-Müllerian hormone (AMH) levels were measured, and ovarian volume (OV) and total antral follicle count (AFC) were assessed by transvaginal sonar in patients and in healthy controls. Analysis was carried out on the association of SLE disease activity with AMH, OV, and AFC. Results: SLE patients had decreased levels of AMH, OV, and AFC, correlating with age, activity, and damage levels of SLE, displaying a negative consequence of SLE. In the SLE group, the CD4+ T cells and natural killer cells were significantly reduced (P < 0.05). Conclusion: AMH levels and AFC were decreased in women with SLE with autoimmune activity and CD8+ T-cell activation; they can be used as useful markers and account for a high proportion of women with low ovarian reserve