Purpose: A prospective intraindividual study to evaluate the effect of flap removal in myopic epi-LASIK surgery on visual rehabilitation and postoperative pain. Methods: Ninety eyes of 45 patients were treated for myopia with epi-LASIK. In each patient, the epithelial flap was repositioned in one eye after epi-LASIK (group 1) while the flap was removed in the other (group 2). Uncorrected visual acuity (UCVA), best corrected visual acuity (BCVA), spherical equivalent (SE) refraction, postoperative pain and corneal haze were examined for 6 months after surgery in both groups. Results: Group 2 had a better UCVA at 4 days and BCVA at 1 week after surgery (p = 0.001, p = 0.043) than group 1. No significant differences were observed between the two groups in terms of UCVA, BCVA, or SE refraction at 1 week and 1, 2 and 6 months. Postoperative pain scores were similar for both groups. In group 2, severe pain (pain level ≧6) was relatively less than in group 1 at 2 h and 12 h after surgery. Corneal haze levels in both groups were not different. Conclusions: Epi-LASIK surgery with flap removal was found to significantly promote re-epithelialization and visual recovery during the early postoperative period. It was also found to be more predictable and less painful than epi-LASIK surgery.