A power supply system is provided that includes a fuel cell as its energy source and has not only high energy density but also high power density and can respond to sharp change in the power consumption with simple means. In a power supply system, a fuel cell is connected to the input terminal of a DC/DC converter, and a lithium-ion secondary battery and a load are connected to the output terminal in parallel. A voltage measurement device that measures the terminal voltage of the secondary battery and a control microcomputer that sets the target output voltage of the converter are provided, and the target output voltage is set slightly higher than the terminal voltage. The fuel cell is operated within a power generation condition offering the highest fuel conversion efficiency.