Purpose. Our main purpose was to compare safety and efficacy in the treatment of progressive keratoconus with “epithelium-on” and “epithelium-off” corneal collagen cross-linking (CXL). Our secondary purpose was to evaluate efficacy of CXL when hypotonic 0.5% riboflavin is used as photosensitizer. Methods. One eye of 20 patients with bilateral progressive keratoconus was randomly treated for “epithelium-on” CXL (group 1) while the fellow eye underwent “epithelium-off” CXL (group 2). Hypotonic 0.5% riboflavin was used in both groups. Visual acuity, refraction, corneal topography, and wavefront aberrometry were evaluated at baseline and after 1, 6, and 12 months. Specular microscopy was performed on 10 patients preoperatively and after 12 months. Postoperative pain was evaluated using a patient questionnaire. Results. Uncorrected and corrected distance visual acuity improved significantly in both groups. Refraction, topography, and aberrometry showed nonsignificant changes from the preoperative status throughout the 12-month follow-up in both groups. Moreover, the outcomes between the groups were comparable at all follow-up points. Endothelial cell-count was stable. Postoperative pain length was shorter in group 1 ( P < 0.001). Conclusion. “Epithelium-on” and “epithelium-off” CXL using hypotonic 0.5% riboflavin were equally safe and effective in stabilization of keratoconus. Topography and aberrometry outcomes in both groups failed to show any significant improvements. This study is registered at ClinicalTrials.gov: NCT01181219.