Objective To compare the clinical outcomes and aberrations of small incision lenticule extraction (SMILE) and femtosecond laser-assisted LASIK (FS-LASIK) for correction of myopia and myopic astigmatism. Methods This prospective, non-randomized, controlled study enrolled 41 patients (41 eyes) who had SMILE surgery and 37 patients (37 eyes) who had FS-LASIK. Uncorrected distance visual acuity and manifest refraction were measured preoperatively and at 1 day, 1 month, and 3 months postoperatively. Corneal aberrations were measured preoperatively and postoperatively at 3 months. Repeated measures analysis of variance, independent t-tests, paired t-tests, and Chi-square tests were used to analyze and compare the collected data for the two surgical groups. Results There was no significant differences in uncorrected distance visual acuity or spherical equivalent between the SMILE and FS-LASIK groups at 1 day, 1 month, or 3 months postoperatively. For the FS-LASIK and SMILE groups, 95% and 98% of the treated eyes were within ±0.50 diopter (D) of spherical equivalent, and there were no significant differences between the two groups. There was also no significant difference between the two groups in the percentage of the uncorrected visual acuity (=5-LogMAR) which was 5.0 or better at any of the time points after operations. Three months after surgery, the high order aberrations, coma, and spherical aberration of cornea in the 6-mm pupil diameter of the SMILE group were 0.54±0.13 µm, 0.29±0.14 µm, and 0.32±0.12 µm, respectively. These values were significantly lower than in the FS-LASIK group, 0.71±0.45 µm, 0.48±0.42 µm, and 0.47±0.38 µm respectively (t=1.60, 2.00, 1.66, all P＜0.05). Conclusion Both SMILE and FS-LASIK resulted in good visual outcomes in the correction of myopia and myopic astigmatism. The SMILE procedure had a lower aberration induction rate.