When a vehicle mounted with a fuel cell system travels using electric power supplied from the system, a predetermined portion forming the system, such as a fuel cell, is prevented from being frozen by the relative wind. The fuel cell system is mounted on a vehicle and has the fuel cell for generating electric power by using fuel gas and oxidized gas as fuel and also has a control section for controlling the system. When the speed of the vehicle is higher than or equal to a predetermined threshold and predetermined conditions determined by physical quantities relating to power generation conditions of the fuel cell are satisfied, the control section determines that freeze prevention processing is necessary even if the fuel cell is generating electric power and performs the processing.