Polypoidal choroidal vasculopathy (PCV) represents a distinct subtype of neovascular age-related macular degeneration (nAMD). PCV is currently managed using intravitreal anti-vascular endothelial growth factor (VEGF) agents such as brolucizumab and aflibercept. This meta-analysis compares the effectiveness of brolucizumab and aflibercept in PCV patients. We systematically searched four electronic databases to identify eligible studies. Data extraction and pooling were performed utilizing the mean difference (MD) or rate ratio (RR) through the generic inverse variance method, with significance determined by a p-value < 0.05 between intervention subgroups. The generic inverse variance analysis method was applied with the employment of the random-effect model when data were heterogeneous. We retrieved 44 studies, 35 were included in the meta-analysis. The analysis compared the efficacy of aflibercept and brolucizumab in patients with nAMD over 3-6 months and 12 months. For best-corrected visual acuity (BCVA), the MD between aflibercept and brolucizumab were -0.11 versus -0.06 at 3-6 months and -0.11 versus -0.04 at 12 months, with no substantial differences (p = 0.58 and p = 0.08, respectively). Regarding polypoidal regression, RR after aflibercept use was 53% versus 70% for brolucizumab at 3-6 months and 47% versus 61% at 12 months, with no significant differences (p = 0.19 and p = 0.31, respectively). In terms of central retinal thickness (CRT), the MDs for aflibercept versus brolucizumab were -129.03 versus -143.93 at 3-6 months and -129.72 versus -145.32 at 12 months, without significant differences (p = 0.62 for both). For central choroidal thickness (CCT) and central foveal thickness (CFT), no significant differences were found between the two interventions at either time point. However, for central macular thickness, brolucizumab demonstrated superiority over aflibercept at 12 months (MD = -119.29 versus -215.00, p < 0.0001). In conclusion, our meta-analysis comparing aflibercept and brolucizumab in PCV revealed no significant differences in BCVA, polypoidal regression, CRT, CCT, and CFT at 6 or 12 months. Overall, both drugs demonstrated comparable efficacy in managing PCV.