Purpose To quantify aniseikonia following intravitreal ranibizumab (IVR) in patients with branch retinal vein occlusion (BRVO) and assess the relationship between aniseikonia and retinal microstructure. Study design Prospective observational study. Methods This study included 50 patients undergoing IVR treatment for unilateral BRVO. The degree of aniseikonia and best-corrected visual acuity (BCVA) was examined, and retinal microstructure was assessed with optical coherence tomography (OCT) before and 1, 2, 3, 4, 5, and 6 months after treatment. Based on OCT images, we assessed central retinal thickness (CRT), presence of the epiretinal membrane, and serous retinal detachment (SRD), as well as status of the external limiting membrane and ellipsoid zone. Results At baseline, mean aniseikonia was − 1.0 ± 2.5%, ranging from − 11.0 to + 6.0%. Nine out of 50 patients had micropsia (18%), one had macropsia (2%), and 40 had no aniseikonia (80%). After 6 months of treatment, mean aniseikonia was − 0.7 ± 1.5%, ranging from − 4.5 to + 3.5%. BCVA significantly improved after treatment (P < 0.001), but aniseikonia did not change (P = 0.73). In patients with BRVO who had micropsia (≤ − 2.0%) at baseline, mean aniseikonia significantly improved from − 4.8 ± 3.3% to − 0.9 ± 1.4% (P < 0.05). Aniseikonia after treatment significantly correlated with BCVA (P < 0.05) and the presence of SRD at baseline (P < 0.05). Conclusion Majority of eyes with aniseikonia in BRVO had micropsia. The BCVA as well as the micropsia improved following treatment with IVR for BRVO. BCVA and the presence of SRD were predictors of post-treatment aniseikonia.