Purpose: To evaluate the effect of long-term effects of hydroxychloroquine (HCQ) use on the corneal endothelium in patients with systemic lupus erythematosus (SLE). Methods: The study included 30 eyes of 15 patients who used HCQ for at least five years and were followed up in the rheumatology clinic for SLE and 29 eyes of 15 patients newly diagnosed with SLE who had not taken any medication. All patients underwent complete ophthalmologic examinations, central corneal thickness measurements, endothelial cell counts and endothelial morphological examinations by specular microscopy. Results: The mean age was 41.25 ± 6.89 years in group 1 and 41.81 ± 5.78 years in group 2 (p = 0.737). The mean corneal endothelial cell density was 2662 ± 184 cells/mm2 in group 1 and 2649 ± 315 cells/mm2 in group 2 (p = 0.843). The percentage of cell hexagonality was 46.6 ± 11.8% in group 1 and 48.7 ± 13.8% in group 2 (p = 0.625). A difference was noted in endothelial cell variation in both groups, at 36.7 ± 6.9% in group 1 and 39.9 ± 6.2% in group 2 (p = 0.057) but not statistically significant. No difference was observed between the two groups in terms of central corneal thickness. The duration of HCQ use was negatively correlated with hexagonality (r = −0.564, p = 0.001) Conclusion: Long-term use of HCQ in SLE patients had no negative effect on endothelial cell density and cell variation, but a negative correlation existed between the duration of HCQ usage and hexagonality.