Purpose: To compare the outcomes of transepithelial photorefractive keratectomy (transPRK) with femtosecond laser assisted in situ keratomileusis (FS-LASIK) for the correction of astigmatism on amblyopic eyes. Methods: The design was a retrospective interventional study on 37 eyes with hyperopic or mixed astigmatism and refractive amblyopia, which underwent transPRK or FS-LASIK. The patients were distributed into 2 groups according to the technique used. Data was collected from patient files and comparison between groups was performed. The main outcomes measured were corrected distance visual acuity (CDVA), sphere, cylinder, spherical equivalent (SEQ), efficiency and safety indexes. Results: In the transPRK group, SEQ improved significantly after 1 month, from 2.08 ± 2.02D (p0.05), sphere improved from 4.03 ± 1.44D preoperatively to 0.67 ± 0.9D at 1 month (p0.05) at the 12 month visit, sphere improved from 4.11 ± 2.35D preoperatively to -0.42 ± 0.66D at 1 month (p<0.05) and further to -0.08 ± 0.75D at 12 months (p<0.05). CDVA also improved from 0.191 ± 0.1 logMAR to 0.140 ± 0.1 logMAR at 1 year. Safety index after 1 month was 1.1 ± 0.2 and 1.16 ± 0.21 at the 1-year visit. Efficiency index was 0.98 ± 0.27 at 1 month and 1.06 ± 0.23 after 1 year. Conclusion: Both procedures were safe and efficient in improving visual acuity for patients with mixed and hyperopic astigmatism and refractive amblyopia. Abbreviations: transPRK = transepithelial photorefractive keratectomy, FS-LASIK = femtosecond laser in situ keratomileusis, logMAR = logarithm of the Minimum Angle of Resolution, BCVA = best corrected distance visual acuity, CDVA = corrected distance visual acuity.