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PURPOSE To evaluate the 2-year clinical outcomes of corneal crosslinking (CXL) using transepithelial iontophoresis CXL (T-ionto CXL) in comparison with standard CXL for the treatment of progressive keratoconus. SETTING Single-site study. DESIGN Randomized controlled clinical trial with identifier code NCT02117999. METHODS The eyes of the participants were randomized to have either T-ionto CXL and/or standard CXL. Assessments of uncorrected (UDVA) and corrected (CDVA) distance visual acuities (logarithm of the minimum angle of resolution [logMAR]), manifest refraction spherical equivalent, maximum simulated keratometry (K) (diopters [D]), corneal higher-order aberrations (HOAs), central corneal thickness (CCT), and endothelial cell density (ECD) were performed at 3 days, 7 days, and 1, 3, 6, 12, and 24 months postoperatively. RESULTS The study comprised 34 eyes (25 patients). There were 22 eyes in the T-ionto CXL group and 12 eyes in the standard CXL group. Two years after T-ionto CXL and standard CXL, the mean maximum K flattened by -1.05 ± 1.20 D (P = .07) (20 eyes) and -1.51 ± .89 D (P < .001) (11 eyes), respectively. Two study cases (10%) and no control showed maximum K steepening of more than 1.0 D at 24 months postoperatively. The mean change in CDVA was -0.08 ± 0.15 logMAR (P = .04) and -0.02 ± 0.06 logMAR (P = .34) after T-ionto CXL and standard CXL, respectively. A significant average decrease in the myopic defocus (+0.81 D; P < .05) was found in both groups. No significant differences in the outcome measures between treatments were found at 24 months. The corneal HOAs, CCT, and ECD values did not change significantly in any group at 2 years postoperatively. CONCLUSIONS Clinically significant topographic, visual, and refractive improvements were found 2 years after T-ionto CXL; standard CXL showed more significant corneal apex flattening than the transepithelial iontophoresis protocol.