Fuel cell systems and methods for controlling fuel cell systems. In one embodiment, the method includes supplying power produced by operating the fuel cell stack in a maximum output mode to the load while concurrently charging the secondary cell with the produced power when an amount of charge of the secondary cell is smaller than a first standard value, supplying both power produced by operating the fuel cell stack in a stable output mode and the power discharged by the secondary cell to the load when the amount of charge of the secondary cell is larger than a second standard value, and maintaining an existing output mode among the output modes when the amount of charge of the secondary cell is larger than the first standard value and smaller than the second standard value.