Fuchs' endothelial corneal dystrophy (FECD) is the occurrence of corneal edema due to endothelial cell dystrophy. Descemet membrane endothelial keratoplasty (DMEK) is considered to be the gold standard of treatment. The aim of this study was to investigate the changes in the corneal epithelial thickness of FECD patients before and after DMEK and to compare these results with a healthy control cohort. In this retrospective analysis, 38 eyes of patients with FECD that were treated with DMEK and 35 healthy control eyes received anterior segment optical coherence tomography (OCT; Optovue, XR-Avanti, Fremont, CA, USA). The corneal epithelial thicknesses in different locations were analyzed and compared between the preoperative, postoperative, and control cohorts. The median follow-up time was 9 months. There was a significant degression of the mean epithelial thickness after DMEK in the central, paracentral, and mid-peripheral zones (p < 0.01) of the cornea. The total corneal thickness and stromal thickness decreased significantly as well. No significant differences were observed between the postoperative and control cohorts. In conclusion, the FECD patients had an increased epithelial thickness compared to the healthy controls, which decreased significantly after DMEK and reached thickness levels comparable to those of healthy control eyes. This study emphasized the importance of distinguishing between the corneal layers in anterior segment pathologies and surgical procedures. Moreover, it accentuated the fact that the structural alterations in FECD extend beyond the corneal stroma.