© 2016, Springer Science+Business Media Dordrecht.The purpose of the study was to evaluate the outcomes and possible complications of CXL performed with customized epithelial debridement technique to keratoconic corneas with the thinnest pachymetry values less than 400 µm. Nineteen eyes of 19 patients were included. The uncorrected (UCVA) and best corrected visual acuity (BCVA), flattest and steepest keratometric (K) readings, central corneal thickness at the thinnest point (t-CCT), endothelial cell density (ECD) were assessed before and 12 months after CXL. The mean UCVA was increased (p = 0.001), while the mean BCVA did not show any difference (p > 0.05). The mean flattest and steepest K readings were decreased (p = 0.001). No change was observed in the mean t-CCT (p > 0.05). The mean ECD was decreased (p = 0.001). The mean pre-CXL and post-CXL percentages of polymegathism and pleomorphism did not show any significant difference (p > 0.05). CXL performed with customized epithelial debridement technique is successful in halting the progression of keratoconus in corneas thinner than 400 µm after 12 months of treatment. However, significant endothelial cell loss can occur after this procedure.