Electrolyzed water mainly containing hypochlorous acid is widely used because of its strong microbicidal effects, biosafety, and eco-friendliness. For frequent use in intraoral treatments, we focused on neutral electrolyzed water (NW) produced using two-stage electrolysis and investigated its storage stability. For standard-concentration NW preparations with a free available chlorine concentration (ACC) of 25, 35, and 50 mg/L and high-concentration NW preparations (100, 200, 300, 500, and 1000 mg/L), the changes in the pH, oxidation reduction potential, and ACC during a 126-day storage period and the bactericidal efficacies after storage were examined. Storage under non-shaded conditions at room temperature (LRT) and a higher ACC substantially altered the properties of the NW. NW (≤300 mg/L) had a pH of 5.9–7.3 even after storage under LRT; however, NW with a higher ACC (500 and 1000 mg/L) had a pH ˂ 5.5, critical for human enamel, even under shaded and refrigerated conditions (SLW). Only NW (25 mg/L) stored under LRT decreased the bactericidal effect (removal rate: 99.8%). When stored for use in intraoral treatments, NW should be prepared with an ACC of 25–300 mg/L and stored in SLW. It is suggested that stored NW, especially when diluting it, should be checked to ensure it maintains the properties appropriate for every intended purpose.