Background This study clinically evaluated the visual outcomes after refractive surgery for myopia using femtosecond laser-assisted in situ keratomileusis (femto-LASIK) and epi-LASIK (flap-off). Methods In this prospective cohort study, 40 eyes of 27 patients were divided into two groups depending on the technique used for refractive surgery. Femto-LASIK flaps and epi-LASIK flaps (flap-off) were created using femtosecond laser and Epi-K TM epikeratome, respectively. Uncorrected distance visual acuity (UDVA), corrected distance visual acuity (CDVA), manifest refraction (MR), corneal asphericity (Q-value), and corneal higher-order aberrations (HOAs) were assessed pre- and postoperatively. Results The improvement in LogMAR UDVA after refractive surgery was statistically significant for both groups ( P < 0.001 for all groups); it was significantly improved in the femto-LASIK group, 1 day and 1 week postoperatively ( P < 0.001, P = 0.019, respectively). With regard to the front and total corneal HOAs, there were significant differences in spherical aberrations (Z 4,0 ) between the femto-LASIK and flap-off epi-LASIK groups ( P = 0.016 and P = 0.017, respectively). With regard to the back corneal HOAs, there were significant differences in vertical coma (Z 3,-1 ) aberration, 0.027 ± 0.027 μm (femto-LASIK) and 0.001 ± 0.034 μm (flap-off epipolis LASIK); horizontal secondary astigmatism (Z 4,2 ) aberration, -0.008 ± 0.012 μm (femto-LASIK) and 0.007 ± 0.018 μm (flap-off epipolis LASIK); oblique tetrafoil (Z 4,-4 ) aberration, -0.008 ± 0.029 μm (femto-LASIK) and 0.015 ± 0.026 μm (flap-off epi-LASIK), respectively ( P = 0.018, P = 0.007, and P = 0.022, respectively). However, the back corneal HOA changes did not have a significant effect on the total corneal HOA changes. Conclusion Femto-LASIK yielded better early visual outcomes than did flap-off epi-LASIK, but there was no significant difference between the outcomes of the two procedures, 1 week postoperatively.