A power supply system P is provided with a fuel cell 1 and a battery unit 2 connected to the fuel cell 1. The battery unit 2 is provided with a first battery 21 connected to the fuel cell 1 so as to supply power to an auxiliary machine 12 of the fuel cell 1 and to be able to be charged with generated power of the fuel cell 1, a second battery 22 connected to the auxiliary machine 12 of the fuel cell 1 through a path p4 different from that of the first battery 21 so as to be able to supply power, and switchers R1, R2 configured to switch the power supply source to the auxiliary machine 12 of the fuel cell 1 between the first battery 21 and the second battery 22.