A fuel cell system includes: a fuel cell; a fuel cell step-up converter having an input terminal, wherein the input terminal is connected to the fuel cell; a secondary cell; a secondary cell step-up converter having an input terminal an output terminal, wherein the input terminal is connected to the secondary cell. wherein the output terminal is connected to an output terminal of the fuel cell step-up converter; and a control device configured to control at least the fuel cell step-up converter and the secondary cell step-up converter to control the fuel cell system, wherein, the control device executes interruption control when the control device executes continuity control and an output of the fuel cell system is requested to be greater than an output of the secondary cell in the continuity control, wherein the continuity control is a control to control the secondary cell step-up converter to output an input voltage from the secondary cell without stepping up the input voltage, wherein the interruption control is a control to interrupt an electrical connection between the fuel cell system and the secondary cell.