Background: Localized macular edema and retinal nerve fiber layer (RNFL) thinning have been reported shortly after laser in situ keratomileusis (LASIK) in adults. However, it is still unclear how LASIK affects the retina of children. This study aimed to investigate the macular retina and RNFL thickness in children with refractive amblyopia who underwent femtosecond laser-assisted LASIK (FS-LASIK). Methods: In this study, we included 56 eyes of 32 patients with refractive amblyopia who underwent FS-LASIK in our hospital from January 2012 to December 2016. Foveal (foveal center retinal, parafoveal retinal, and perifoveal), macular inner retinal (superior and inferior), and peripapillary RNFL thicknesses (superior, inferior, temporal, and nasal) were measured using Fourier-domain optical coherence tomography before surgery and 1 day, 3 days, and 1 week after surgery. We divided these patients into three groups based on their refractive error: High myopic group with 22 eyes (equivalent sphere, > 6.00 D), mild myopic group with 19 eyes (equivalent sphere, 0-6.00 D), and hyperopic group with 15 eyes (equivalent sphere, >+0.50 D). We compared the macular retina and RNFL thickness before and after LASIK. A paired simple t-test was used for data analysis. Results: One week after surgery, the visual acuity for all 56 eyes of the 32 patients reached their preoperative best-corrected vision. Visual acuity improved two lines or better for 31% of the patients. The residual refractive errors in 89% of the patients were within +/- 0.5 D. In the high myopic group, the foveal center retinal and parafoveal retinal thicknesses were thicker 1 day and 3 days after surgery than before surgery (t = 2.689, P = 0.012; t = 2.383, P = 0.018, respectively); no significant difference was found 1 week after surgery (P > 0.05). The foveal center retinal and parafoveal retinal thicknesses were greater 1 day after surgery than they were before surgery (P = 0.000 and P = 0.005, respectively) in the mild myopic and hyperopic groups. No significant difference was found 3 days or 1 week after surgery (P > 0.05). In all three groups, no significant difference was found in the macular inner retinal or peripapillary RNFL thickness 1 day, 3 days, or 1 week after surgery (P > 0.05). Conclusions: The foveal center retinal edema after FS-LASIK is mild and reversible in children, that mostly occurred in the high myopic group with no effect on the visual acuity, and is always relieved within 1 week.