A fuel cell system includes a fuel cell, a water storage unit configured to store water recovered from the fuel cell and be able to drain the stored water, a water usage unit configured to use the water in the water storage unit, and a control unit configured to control a drain of the water from the water storage unit. The control unit is configured to, when a first predetermined time has elapsed since a last drain of the water from the water storage unit, drain the water from the water storage unit. The control unit is configured to, when it is predicted that the water in the water storage unit is used by the water usage unit within a second predetermined time shorter than the first predetermined time, not drain the water from the water storage unit even when the first predetermined time has elapsed since the drain of the water from the water storage unit.