A system for operating a positive temperature coefficient (PTC) heater in a fuel cell vehicle includes a fuel cell stack and a PTC heater generating heat when supplied with an electric current. A controller is configured to check a key-start state of the vehicle and determine whether or not an outdoor temperature is lower than a reference temperature. If it is determined that the vehicle is key-started so as to activate the fuel cell stack, and the outdoor temperature is lower than the reference temperature, the controller supplies electrical energy generated by the fuel cell stack to the PTC heater, thereby driving the PTC heater.