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To evaluate and compare the effectiveness and safety of accelerated transepithelial (A-epi-on) corneal collagen cross-linking (CXL) with standard CXL (epi-off) for children with progressive keratoconus.Prospective, cohort study including 61 eyes of 51 patients younger than 18 years with progressive keratoconus at Oftalmosalud Instituto de Ojos, Lima, Peru. A-epi-on CXL was performed for 36 eyes using 30 minutes of impregnation (0.25% riboflavin, 1.0% phosphate hydroxypropyl methylcellulose, 0.007% benzalkonium chloride) and 5 minutes of irradiation (18 mW/cm2). Epi-off CXL was performed for 25 eyes using 30 minutes of impregnation (riboflavin 0.1% solution plus 20% dextran 500) and 30 minutes of irradiation (3 mW/cm2). Scheimpflug imaging parameters were evaluated preoperatively and at 6 and 12 months postoperatively.Mean uncorrected visual acuity improvement was 0.12 logarithm of the minimum angle of resolution (logMAR) for both groups (P = 0.09 for A-epi-on and P = 0.16 for Epi-off). Mean improvements in the best-corrected visual acuity were 0.09 logMAR (P = 0.05) and 0.06 logMAR (P = 0.05) at 12 months postoperatively for the A-epi-on group and the epi-off group, respectively. Mean maximum keratometry changes were +0.1 D (P = 0.62) and −0.94 D (P = 0.11) for the A-epi-on group and the epi-off group, respectively, at 12 months postoperatively. There were no significant differences between groups regarding changes in pachymetry and posterior elevation values (P > 0.05). Keratoconus progression was observed in 5.6% and 12% of eyes in the A-epi-on group and the epi-off group, respectively.Accelerated epi-on CXL and standard epi-off CXL are safe and effective for stopping the progression of keratoconus at 12 months postoperatively.