Several conflicting results regarding the efficacy of 0.01% atropine in slowing axial elongation remain in doubt. To solve this issue and evaluate the safety of 0.01% atropine, we conducted a systematic review and meta-analysis with the latest evidence. The review included a total of 1178 participants (myopic children). The efficacy outcomes were the mean annual progression in standardized equivalent refraction (SER) and axial length (AL). The safety outcomes included mean annual change in accommodative amplitude, photopic and mesopic pupil diameter. The results demonstrated that 0.01% atropine significantly retarded SER progression compared with the controls (weighted mean difference [WMD], 0.28 diopter (D) per year; 95% confidence interval (CI) = 0.17, 0.38; p < 0.01), and axial elongation (WMD, −0.06 mm; 95% CI = −0.09, −0.03; p < 0.01) during the 1-year period. Patients receiving 0.01% atropine showed no significant changes in accommodative amplitude (WMD, −0.45 D; 95% CI = −1.80, 0.90; p = 0.51) but showed dilated photopic pupil diameter (WMD, 0.35 mm; 95% CI = 0.02, 0.68; p = 0.04) and mesopic pupil diameter (WMD, 0.20 mm; 95% CI = 0.08, 0.32; p < 0.01). In the subgroup analysis of SER progression, myopic children with lower baseline refraction (>−3 D) and older age (>10-year-old) obtained better responses with 0.01% atropine treatment. Furthermore, the European and multi-ethnicity groups showed greater effect than the Asian groups. In conclusion, 0.01% atropine had favorable efficacy and adequate safety for childhood myopia over a 1-year period.