A cooling method for a fuel cell using a heat exchanger is provided. The method comprises the steps of: providing an ion exchanger in a circulation system for the cooling fluid; decreasing ion concentration in the cooling fluid by circulating the cooling fluid through the fuel cell and the ion exchanger when the temperature of the cooling fluid is below a thermostat operating temperature; distributing a portion of the cooling fluid discharged from the fuel cell, mixing the portion of the cooling fluid returning from the heat exchanger with another portion of the cooling fluid whose ion concentration has been decreased in the previous step, and returning the cooling fluid mixture to the fuel cell, when the temperature of the cooling fluid is approaching the thermostat operating temperature; and cooling the fuel cell by circulating the cooling fluid through the fuel cell and the heat exchanger after the temperature of the cooling fluid reaches the thermostat operating temperature. By using this cooling method, the cooling fluid having a high conductivity is not distributed to the fuel cell.