Objective To investigate the thicknesses of the ganglion cell-inner plexiform layer (GC-IPL) and retinal nerve fiber layer (RNFL) of the fellow eyes of patients with unilateral exudative age-related macular degeneration (AMD). Methods A total of 107 patients with unilateral exudative AMD [34 of typical choroidal neovascularization (tCNV), Group A; 73 of polypoidal choroidal vasculopathy (PCV), Group B] and 73 normal control eyes (Group C) were included. Drusen and subretinal drusenoid deposits were assessed in all participants using fundus photography, autofluorescence, and optical coherence tomography (OCT). The GC-IPL and RNFL thicknesses were measured using Cirrus HD-OCT and compared among groups. Linear regression analyses were used to evaluate the factors associated with GC-IPL thicknesses. Results The average GC-IPL thicknesses of Groups A, B, and C were 77.09 ± 3.87, 80.10 ± 6.61, and 80.88 ± 6.50 μm, respectively (p = 0.022). Sectoral GC-IPLs and central macular thicknesses (CMTs) were significantly different among groups (all, p <0.05), whereas none of the RNFL parameters differed significantly (all, p >0.05). Multivariate linear regression analyses revealed that age (p <0.001), CMT (p <0.001), and tCNV (p = 0.013) were significantly associated with average GC-IPL thickness, and the rate of reduction of GC-IPL thickness with increasing age in the fellow eyes of tCNV patients was higher than those in the PCV and control groups.