To evaluate correlations between persistent macular edema associated with branch retinal vein occlusion (BRVO) and the macular perfusion status in the superficial capillary plexus (SCP) and deep capillary plexus (DCP) using optical coherence tomography angiography (OCTA). Retrospective, case-control study. Twenty patients with BRVO followed for 12 months or more were enrolled. Persistent macular edema was defined as central retinal thickness exceeding 300 μm that persisted or recurred less than 3 months after the final treatment. We compared two groups (i.e., seven eyes with persistent macular edema and 13 eyes without macular edema). The macular perfusion status was evaluated using OCTA. We defined a gap vessel as a residual vessel in the SCP that existed simultaneously with capillary loss in the DCP. The gap vessels were determined by subtracting the vessel images of the DCP from the images of the SCP using an image processing technique. In eyes with persistent macular edema, the area with gap vessels was significantly (P = 0.0013) larger than in eyes without macular edema (14.34% vs. 8.02%). Other factors evaluated (i.e., the area of the foveal avascular zone, superficial vessel density, and deep vessel density) did not differ significantly (P = 0.66, P = 0.23, P = 0.34, respectively) between the groups. The difference in capillary loss between the SCP and DCP can facilitate development of persistent macular edema in BRVO.