We investigated changes in multifocal visual evoked potential (mfVEP) responses due to beta-zone parapapillary atrophy (βPPA). Patients with glaucomatous optic neuropathy (GON) with or without standard achromatic perimetry (SAP) abnormalities were referred for mfVEP testing during a 2-year period. Eyes with good quality optic disc stereophotographs and reliable SAP results were included. The mfVEP monocular mean latency delays (ms) and amplitudes (SNR) were analyzed. Age, SAP mean deviation (MD), pattern standard deviation (PSD), and spherical equivalent (SE) were analyzed in the multivariate model. Generalized estimated equations were used for comparisons between groups after adjusting for inter-eye associations. Of 394 eyes of 200 patients, 223 (57%) had βPPA. The βPPA eyes were older (59.6 ± 13.7 vs. 56.5 ± 13.7 year, P = 0.02), more myopic (−4.0 ± 3.5 vs. −1.3 ± 3.5 D, P < 0.01), and had poorer SAP scores (MD: −4.9 ± 5.2 vs. −2.6 ± 5.2 dB, P < 0.01; PSD: 4.3 ± 2.9 vs. 2.5 ± 3.0 dB, P < 0.01). By univariate analysis, mean latencies were longer in βPPA eyes (6.1 ± 5.3 vs. 4.0 ± 5.5 ms, P < 0.01). After adjusting for differences in SE, age, and SAP MD, there was no significant difference between the two groups (P = 0.09). βPPA eyes had lower amplitude log SNR (0.49 ± 0.16 vs. 0.56 ± 0.15, P < 0.01), which lost significance (P = 0.51) after adjusting for MD and PSD. Although eyes with βPPA had significantly lower amplitudes and prolonged latencies than eyes without βPPA, these differences were attributable to differences in SAP severity, age, and refractive error. Thus, βPPA does not appear to be an independent factor affecting mfVEP responses in eyes with GON.