There are some sensitive problems with developing Fuel Cell Vehicle. One of them is cooling system. As a lot of researchers already know, the coolant temperature of Fuel Cell Vehicle is lower than Internal Combustion Engine Vehicle. For this reason, cooling system of Fuel Cell Vehicle should have high flow water pump, extensive radiator and high power fan motor to maintain constant temperature level. Among these units, we have focused on high power fan motor which is operated by high voltage. As a result, we had developed HV BLDC fan motor using hall sensor. One step further, this paper presents the sensorless control on HV BLDC fan motor. Through this study, we have got equivalent performance compared to HV sensor type BLDC fan motor.