During the COVID-19 pandemic, intravitreal injections are performed with patients wearing masks. The risk of endophthalmitis after intravitreal injection is reported to increase due to an influx of exhaled air containing oral bacteria from the upper part of the mask onto the ocular surface. We retrospectively investigated the incidence of endophthalmitis when intravitreal anti-vascular endothelial growth factor (anti-VEGF) injections were performed using the same infection control measures before and during the pandemic. Vitreoretinal specialists performed intravitreal injections of anti-VEGF agents in the outpatient room of a university hospital. Infection control measures before and during the pandemic included covering the patient’s eye with adhesive face drape and irrigating the ocular surface with 0.25% povidone-iodine before draping, and immediately before and after injection. Before the COVID-19 pandemic (February 2016 to December 2019), one case of endophthalmitis occurred among 31,173 injections performed (0.0032%; 95% confidence interval (CI), 0.000008–0.017872%). During the COVID-19 pandemic (January 2020 to August 2021), one case of endophthalmitis occurred among 14,725 injections performed (0.0068%; 95% CI, 0.000017–0.037832%). There was no significant difference between the two periods (Fisher’s exact test: p = 0.5387). Even during the COVID-19 pandemic, very low incidence of endophthalmitis after intravitreal injection can be maintained by implementing basic infection prophylactic measures, including face draping and 0.25% povidone-iodine irrigation, established before COVID-19 pandemic.