Purpose Our purpose was to compare the efficacy of ‘epithelium-off’ and ‘epithelium-on’ cross-linking (CXL) in treatment of progressive keratoconus. Patients and methods This study included 48 eyes of 26 patients who met our inclusion criteria. The Epi-Off CXL group included 32 eyes of 17 patients, and the Epi-On CXL group included 16 eyes of nine patients. Preoperative assessments of uncorrected and best-corrected visual acuities, refractive errors, keratometry, and corneal tomography including pachymetry, were compared with the postoperative values. Results Preoperatively, there was a statistically nonsignificant difference between the two groups in all studied variables except for the pachymetry at thinnest location. In the Epi-Off group, there was a significant improvement of uncorrected visual acuity, best-corrected visual acuity, Kmax, and inferior–superior value at the 12-month visit. There was late significant worsening of the back elevation and spherical equivalent at the 12-month visit and also significant thinning of pachymetry at thinnest location associated with significant worsening of the average thickness increase. All other variables showed nonsignificant change (stabilization) at both postoperative visits. In the Epi-On group, there was significant thinning of pachymetry at thinnest location and stabilization of uncorrected corrected visual acuity, best-corrected visual acuity, K1, Kmax, (inferior–superior), Y-coordinate, and front elevation at both postoperative visits, and early stabilization with late worsening of all of other variables. Conclusion The Epi-Off CXL was found to be more superior to Epi-On CXL in terms of stabilization of progressive keratoconus but was inevitably associated with complications related to epithelial debridement.