There are provided a method and apparatus for manufacturing hydrogen-containing drinking water that can fill a packaging container with hydrogen-containing water while suppressing the change of the dissolved hydrogen concentration of the hydrogen-containing water to a low level.A method of continuously manufacturing hydrogen-containing drinking water includes (A) a deaeration step, (B) a hydrogen dissolving step, (C) a filling step, and (D) a sealing step. Pressure is applied to water flow channels corresponding to hydrogen-containing water, which is to be injected to a packaging container in the filling step, from purified water that is to be supplied to the deaeration step. The filling step includes: a preparation stage of supplying hydrogen-containing water, to which pressure is applied, into a filling device； a deaeration stage of removing gas, which is present in the packaging container, after connecting the packaging container to the filling device； an injection stage of directly injecting the hydrogen-containing water, to which pressure is applied, into the packaging container； and a discharge stage of discharging hydrogen-containing water, which remains in the filling device, into the packaging container by introducing pressurized air into the filling device. The method further includes a step of immediately proceeding to the sealing step (D) when the injection port and the filling port are disconnected from each other.
