One of the concepts for the design of a highly proton-conductive perovskite-type oxide is to increase the proton concentration. In this study, we focused on Ba–Sc oxide known for its brownmillerite-type structure and great potential for a high proton concentration. To achieve the highly hydrated phase, high-pressure synthesis was conducted using hydroxide as the H2O source. Although the expectation was that perovskite-type BaScO2(OH) would simply be a hydrated phase, the formation of Sc vacancies increased resulting in the greater hydration of the Ba–Sc oxide. It was likely that the fully hydrated phase was perovskite-type BaSc0.67O­(OH)2. One third of the Sc sites were vacant, and the effective charge of Sc vacancies were compensated by the excess protons. First principles calculation revealed that the protons residing in the Sc vacancies were orientated toward a Sc vacancy and compensated the B-site charge in a manner similar to that of hydrogarnet substitution. This B-site deficiency caused by the extensive hydration condition is a novel mechanism to increase the proton concentration of perovskite-type proton conductors. The electrical conductivity, 10–2 S·cm–1 at 450–500 °C, was comparable to that of acceptor-doped BaZrO3, although the conductivity discontinuously changed at dehydration temperature.