This invention provides a power supply system for supplying electrical power to a load. The system includes: a first and a second power supply wirings for a connection to the load; a fuel cell system having a fuel cell connected between the first and second power supply wiring; a secondary power supply system connected in parallel to the fuel cell between the first power supply wiring and the second power supply wiring; a switch for opening and closing the connection between the fuel cell and the first power supply wiring; a countercurrent prevention device connected between the fuel cell and the first power supply wiring; and a controller for controlling the secondary power supply system and the switch. The controller controls the secondary power supply system to boost a terminal voltage of the secondary power supply system to a first voltage, when connecting the fuel cell to the first power supply wiring. The first voltage is equal or higher than an electrical potential difference of the open terminals of the fuel cell.