This systematic review was to compare the clinical outcomes between laser-assisted subepithelial keratectomy (LASEK) and laser in situ keratomileusis (LASIK) for myopia. Primary parameters included mean manifest refraction spherical equivalent (MRSE), MRSE within ±0.50 diopters, uncorrected visual acuity (UCVA) ≥20/20, and loss of ≥1 line of best-corrected visual acuity (BCVA). Secondary parameters included flap complications and corneal haze. Twelve clinical controlled trials were identified and used for comparing LASEK (780 eyes) to LASIK (915 eyes). There were no significant differences in visual and refractive outcomes between the two surgeries for low to moderate myopia. The incidence of loss of ≥1 line of BCVA was significantly higher in moderate to high myopia treated by LASEK than LASIK in the mid-term and long-term followup. The efficacy (MRSE and UCVA) of LASEK appeared to be a significant worsening trend in the long-term followup. Corneal haze was more severe in moderate to high myopia treated by LASEK than LASIK in the mid-term and long-term followup. The flap-related complications still occurred in LASIK, but the incidence was not significantly higher than that in LASEK. LASEK and LASIK were safe and effective for low to moderate myopia. The advantage of LASEK was the absence of flap-related complications, and such procedure complication may occur in LASIK and affect the visual results. The increased incidence of stromal haze and regression in LASEK significantly affected the visual and refractive results for high myopia.