Purpose To investigate the effect of intravitreal anti-vascular endothelial growth factor (VEGF) injections on ganglion cell-inner plexiform layer (GCIPL) thickness in patients with age-related macular degeneration (AMD). Methods This retrospective study included patients with continuous anti-VEGF treatment who were administered at least three consecutive injections for unilateral neovascular AMD. The GCIPL thickness of the study eyes was compared before and after treatment and with healthy fellow eyes using spectral-domain optical coherence tomography. We also evaluated best-corrected visual acuity, age, and intraocular pressure. Results In total, 96 eyes of 48 patients (14 females and 34 males; mean ± standard deviation [SD] age, 70.10 ± 8.89 years) with mean number of 6.29 (SD ± 3.76) anti-VEGF injections and a mean follow-up period of 24.93 months (SD ± 19.86) were included in the study. After three consecutive intravitreal injections of anti-VEGF, the mean GCIPL thickness was significantly reduced from 70.50 (SD ± 14.06) to 65.97 (SD ± 13.91) µm. Borderline or nonsignificant decrease was also observed in GCIPL thickness for each sector. At the end of the study, the mean GCIPL thickness was further reduced to 62.56 (SD ± 16.30) µm, and significant decreases were also observed in all other sectors compared with baseline. Conclusions It has been observed that GCIPL thickness can decrease with only three consecutive anti-VEGF injections as well as with long-term treatment in AMD patients.