To provide a reliable hydrogen generating system and fuel cell system which can stably operate even in a use environment below a freezing point.

The hydrogen generating system includes: a hydrogen generating material holding vessel 1 which holds a hydrogen generating material 1a which generates hydrogen 1c by the reaction with water 1b; a water holding vessel 2 which holds the water 1b; a pump 3 which supplies the water 1b in the water holding vessel 2 into the hydrogen generating material holding vessel 1 through a water supply tube 12; and a blower 5 which removes water which remains in the water supply tube 12 after stopping the water supply with the pump 3.