Esophagogastroduodenoscopy (EGD) has a high risk of virus transmission during the current coronavirus disease 2019 era, and preventive measures are under investigation. We investigated the effectiveness of a newly developed patient-covering negative-pressure box system (Endo barrier®) (EB) for EGD. Eighty consecutive unsedated patients who underwent screening EGD with EB use were prospectively enrolled. To examine the aerosol ratio before, during, and after EGD, 0.3- and 0.5-μm aerosols were measured every 60 s using an optical counter. Moreover, the degree of contamination of the examiners’ goggles and vinyl gowns was assessed before and after EGD using a rapid adenosine triphosphate (ATP) test for simulated droplets. Data were available in 73 patients and showed that 0.3- and 0.5-μm particles did not increase in 95.8% (70/73) and 94.5% (69/73) of patients during EGD under EB. There were no significant differences in the total 0.3- or 0.5-μm particle counts before versus after EGD. The difference in the ATP levels before and after EGD was −0.6 ± 16.6 relative light units (RLU) on goggles and 1.59 ± 19.9 RLU on gowns (both within the cutoff value). EB use during EGD may provide a certain preventive effect against aerosols and droplets, decreasing examiners’ exposure to viruses.