Background/Objectives: We intended to investigate choroidal blood flow (CBF) and choroidal thickness (CT) alternations in treatment-naive eyes with non-ischemic branch retinal vein occlusion (BRVO) following intravitreal aflibercept injection (IVA). Methods: Twenty eyes of 20 patients with treatment-naive non-ischemic BRVO, treated with IVA 1+ pro re nata, were included in this study. In the BRVO eyes, CBF and CT were measured in the occlusive region, subfovea, as well as the non-occlusive region, via laser speckle flowgraphy (LSFG) and enhanced depth-imaging optical coherence tomography over a 6-month follow-up period. CBF was analyzed via the mean blur rate using LSFG analysis software (version 3.10.0). Results: CT showed significant reductions in both the occlusive and subfoveal region at 1 week and 1 month after treatment (both p p < 0.05). The mean number of IVA injections during the 6-month period was 1.95 ± 0.6. Conclusions: Aflibercept treatment reduced CBF and CT in addition to a decrease in retinal thickness. These changes at each region might be associated with the improvement of macular edema in BRVO eyes.