Bacterial infection associated with the use of medical or dental devices is a serious concern. Although devices made of ethylene vinyl acetate (EVA) are often used in the oral cavity, there are no established standards for their storage. We investigated bacterial survival on EVA sheets under various storage conditions to establish a standard for hygienic storage of such dental devices. Bacterial counts were evaluated, which showed a significant decrease after washing with sterilized water, mechanical brushing and rinsing, and using Mouthguard Cleaner as compared to untreated samples. In addition, no bacteria were detected on samples stored 2 days or longer in a ventilated environment, whereas they were detected for up to 14 days on samples without any cleaning stored in a closed environment. Bacterial counts for the untreated samples gradually declined, while surviving bacteria on samples treated with sterilized water and mechanical brushing showed a rapid decrease. Additionally, bacterial identification using polymerase chain reaction (PCR) revealed that Streptococcus oralis was dominantly detected on salivary samples after 14 days of storage among both two subjects. For effective hygienic storage of dental devices made of EVA, washing with sterilized water is important to remove absorbed salivary compounds along with storage in a ventilated environment.