A fuel cell system repeats first processing and second processing when the system is started. In the first processing, a control section controls an electric power distribution section so that electric power generated by a fuel cell stack is supplied to accessories and a secondary battery. In the second processing, the control section controls the electric power distribution section so that electric power generated by the fuel cell stack and electric power discharged from the secondary battery are supplied to the accessories. An electric power calculation means of the control section calculates electric power generation by the fuel cell stack and inputs an output command, representing electric power, into air compressor drive/control means. The electric power calculation means gradually changes the magnitude of electric power generation by the fuel cell stack, represented by the output command, at the time of transition between the first processing and the second processing.