Acne scarring is a common disfiguring complication of acne, and fractional lasers are widely applied in improving it. This study is to compare the efficacy and safety of fractional non-ablative 1927 nm thulium laser (FTL) and fractional ablative 2940 nm Er:YAG laser (FEL) in the treatment of acne scarring. Subjects with moderate or severe atrophic facial acne scarring received 3 sessions of FTL on the left side of face and FEL on the right side of face at an average interval of 4-6 weeks. Major assessments included Goodman&Baron quantitative global scarring grading system (GBS), self-rated improvement and satisfaction score. Twenty-seven subjects completed the study; for FTL side, average GBS decreased from 11.15 ± 5.04 at baseline to 7.07 ± 4.87 with an improvement percent of 36.54%; for FEL side, average GBS decreased from 10.81 ± 4.46 to 7.00 ± 4.07 with an improvement percent of 35.27%. Adverse effects include transient pain, erythema, edema, and increase of acne. No significant difference was found between two lasers. Both FTL and FEL improved atrophic acne scarring and were well-tolerated. Increase of acne during laser treatment may have a negative impact on efficacy. Trial registration number was NCT04813419 and date of registration was 19th, March, 2021, retrospectively registered.