To evaluate the change of epithelial and flap thickness after femtosecond laser-assisted in situ keratomileusis (LASIK) using spectral-domain optical coherence tomography (SD OCT) in correlation with the spherical equivalent refraction treated and clinical outcomes. Prospective, randomized, contralateral-eye study. Forty myopic eyes underwent LASIK using an excimer laser with refraction ranging from -1.00 to -7.25 diopters (mean -3.25±1.9). Flap creation was randomized between eyes, using the IntraLASE FS60 laser (IL) in 1 eye and WaveLight FS200 laser (FS) in the contralateral eye. SD OCT was used to evaluate the epithelial and flap thickness profiles and corneal power preoperatively and at 1 week and 1, 3, and 9 months postoperatively. Manifest and wavefront refractions were performed at each postoperative visit. Statistically significant epithelial thickening was observed in both IL and FS groups as early as 1 month postoperatively (P=.033 and P=.042), but this stabilized between 3 (P=.042 and P=.035) and 9 months (P=.043 and P=.041). Femtosecond-LASIK flaps were thicker in the IL group in comparison to the FS group at 3 and 9 months postoperatively (P=.003 and P=.005, respectively). There was a statistically significant correlation between the magnitude of preoperative myopic refraction and the central epithelial thickness at 1, 3, and 9 months (Pearson correlation coefficients 0.485, 0.587 and 0.576) (P=.0021, P=.0010, and P=.0011), respectively. SD OCT corneal power maps showed steepening at 3 and 9 months along with mild myopic shift. Progressive epithelial and flap thickening with increased corneal power were observed after femtosecond laser-assisted in situ keratomileusis for myopia with consequent stabilization between 3 to 9 months postoperatively. The magnitude of epithelial and flap thickness remodeling correlated to the preoperative myopic refractive error.