The authors performed a retrospective and comparative study to compare the efficacy of intravitreal aflibercept and bevacizumab for patients with myopic choroidal neovascularization (mCNV). The patients with treatment-naïve mCNV received 1 + PRN intravitreal bevacizumab from March 2008 to February 2013, while from March 2013 to July 2016 patients were treated by 1 + PRN intravitreal aflibercept, all with monthly follow-up for 12 months. Primary outcome measures included change in central foveal thickness (CFT) in 1 mm by spectral-domain optic coherence tomography, and best corrected visual acuity (BCVA) at month 12. Complications after injections were recorded. The intra-group changes in CFT and BCVA were compared with Wilcoxon signed rank test, the between-group difference compared with Wilcoxon rank sum test. Fisher’s exact test was used for categorical comparison between groups. Seventy-eight eyes of 78 patients were collected. There were 42 eyes in bevacizumab group, with mean age of 53.2 ± 5.4 years and 27 female patients of them. The mean BCVA significantly improved from baseline 0.56 ± 0.35 logMAR to 0.35 ± 0.35 logMAR at Month 12 after bevacizumab treatment (p < 0.001). The mean CFT significantly decreased from baseline 315.3 ± 25.6 μm to 253.7 ± 24.4 μm at Month 12 following intravitreal bevacizumab (p < 0.001). There were 36 eyes in aflibercept group, with mean age of 52.8 ± 6.8 years and 24 female patients of them. The mean BCVA significantly improved from baseline 0.61 ± 0.47 logMAR to 0.38 ± 0.41 logMAR at Month 12 after aflibercept treatment (p < 0.001). The mean CFT significantly decreased from baseline 328.2 ± 19.8 μm to 241.8 ± 27.2 μm at Month 12 following intravitreal aflibercept (p < 0.001). The baseline demographics, lens status, axial length, refractive errors, duration of symptoms, BCVA, and CFT did not differ significantly between groups (p > 0.05). There was no significant difference between bevacizumab and aflibercept groups in BCVA and CFT from Month 1 to Month 12 (p > 0.05). Injection number of aflibercept was 2.11 ± 0.41, less than that of bevacizumab (3.23 ± 0.38) during 12-month period (p = 0.01). There were no systemic thromboembolic event, elevated intraocular pressure, retinal detachment, or infectious endophthalmitis following injections in both groups. We concluded that both aflibercept and bevacizumab can effectively treat choroidal neovascularization in high myopes. Intravitreal aflibercept had similar efficacy but less treatment number than bevacizumab for mCNV during 12-month period.