Background The purpose of this study was to investigate changes in best-corrected visual acuity (BCVA), central macular thickness (CMT) and subfoveal choroidal thickness (SCT) after intravitreal aflibercept injections for neovascular age-related macular degeneration (NV-AMD). Methods Eighty-nine eyes (48 treatment naive, 41 resistant) were included in this prospective study. All patients were treated with three consecutive monthly injections then every two months as required. BCVA, CMT and SCT were recorded and compared within and between the two groups. Results The mean increase in BCVA after injections was 0.18 +/- 0.34 logMAR in the naive group (p = 0.01) and 0.092 +/- 0.38 logMAR in the resistant group (p = 0.131). The mean decrease in CMT was 200.3 +/- 216.1 mu m in the naive group and 183.3 +/- 203.4 mu m in the resistant group (p < 0.001 for both). The mean decrease in SCT was 22.1 +/- 62.0 mu m in the naive group (p = 0.014). The mean change in SCT was 22.28 +/- 74.05 mu m in the resistant group; this was not statistically significant (p = 0.061). Conclusion BCVA, CMT and SCT decreased significantly after intravitreal aflibercept injections in naive patients with NV-AMD. Despite anatomic success, functional improvement was not reached and SCT did not significantly decrease after intravitreal aflibercept injections in resistant patients.