A fuel cell system for a vehicle includes: a fuel cell; a plurality of loads that consumes power generated by the fuel cell and includes a vehicle driving motor; a secondary battery configured to be charged with excess power when an amount of power generated by the fuel cell is greater than an amount of power consumed by the loads and to discharge shortage power when the amount of power generated by the fuel cell is less than the amount of power consumed by the loads; and a control unit configured to control the amount of power generated by the fuel cell such that an amount of charging-discharging power of the secondary battery is maintained at a predetermined value.