Objective To compare patients' subjective postoperative pain, rate of reepithelialization as well as visual and refractive recovery between custom transepithelial ablation and photorefractive keratectomy (PRK) with mechanical epithelial removal. Methods This prospective non-randomized consecutive case control study was comprised of 30 eyes (group 1) treated with custom transepithelial ablation with a iVIS-Suite 100 Hz laser, with deepithelialization integrated within the excimer laser ablation and 30 eyes (group 2) treated with PRK with a Wavelight Allegretto 400 Hz laser with Amoils brush deepithelialization between March 18, 2009 to October 28, 2009. Postoperative pain and reepithelialization were measured every 24 hours postoperatively until full recovery. Patients' refraction, uncorrected visual acuity (UCVA) and best spectacle-corrected visual acuity (BSCVA) were measured weekly during the first month postoperatively. An independent samples Wilcoxon rank sum test was used to assess the difference of patients' subjective postoperative pain between the 2 groups, and an independent samples t test was used to assess the difference of the other parameters. Results The mean reepithelialization time was (2.63±0.49)days and (2.93±0.64)days for group 1 and group 2, respectively (t=2.039, P=0.046). Pain score in group 1 was lower than group 2 (Z=-3.535, P＜0.01) 2 days postoperative. Both maximum and average subjective pain scores were lower in group 1 (Z=-2.261, P=0.024; Z=-2.982, P=0.003) 3 days postoperative. The mean UCVA on the third postoperative week was -0.068±0.088 (logMAR) for group 1 and -0.024±0.069(IogMAR) for group 2 (t=2.236, P=0.030). There were no significant differences in postoperative spherical equivalent or BSCVA between the 2 groups. Conclusion Integrated custom transepithelial ablation seems to result in faster reepithelialization and UCVA recovery as well as lower postoperative pain than PRK with mechanical epithelial removal, while the BSCVA and refractive outcomes are comparable.