Purpose To evaluate the effects of fluorescein dye on corneal endothelial morphology (CEM) after fundus fluorescein angiography (FFA) in patients with diabetic macular edema (DME). Methods In this retrospective study, patients were divided into two groups, nonproliferative diabetic retinopathy (Group-1, NPDR) and proliferative diabetic retinopathy (Group-2, PDR). CEM properties including endothelial cell density (ECD), coefficient of variation of cell area (CV), average cell area (AVG), percentage of hexagonal cells (HEX), and central corneal thickness (CCT) were measured before FFA and at week 1 and month 1 after FFA were collected from patients’ charts. Results The study consisted of 48 patient’s 48 eyes in Group-1 and 50 patient’s 50 eyes in Group-2. In both groups, the mean ECD, CV, AVG, HEX, and CCT measurements at week 1 and month 1 after FFA did not differ statistically from the mean measurements before FFA (p > 0.05). The mean ECD measurements in Group-1 were higher than that in Group-2 and showed statistically significant differences among the groups (p < 0.01 for all). In the Pearson correlation analysis in Group-1, there was no statistically significant relationship between best-corrected visual acuity (BCVA) and (intraocular pressure) IOP values and ECD, AVG, CV, HEX, and CCT measurements (except central macular thickness [CMT] and HEX) before FFA, at week 1 and month 1 after FFA (p > 0.05). In Group-2 there was no statistically significant relationship between BCVA, IOP, and CMT measurements and ECD, AVG, CV, HEX, and CCT measurements before FFA, at week 1 and month 1 after FFA (p > 0.05). Conclusions There is no significant change in CEM after FFA in patients with NPDR and PDR with DME.