A hybrid power supply system having a fuel cell and a secondary power storage device is used as the power source of a drive motor for a motorcycle. Oxygen supplied from an air blower and hydrogen gas supplied from a hydrogen tank react with each other in the fuel cell to generate electric power. In a warm-up mode, where a temperature of the fuel cell is below a threshold temperature, the fuel cell generates more power than is to be consumed by the drive motor, and the surplus power is used to charge the secondary power storage device. In a normal operation mode, after the warm-up of the fuel cell is completed, the electric power generated by the fuel cell is smaller than the power consumed by the drive motor, and the secondary power storage device supplements the power provided by the fuel cell to meet the power requirement of the drive motor. The hybrid power supply system thus decreases the time needed to warm-up the fuel cell and uses the electric power generated by the fuel cell more efficiently.