A fuel cell cooling system may include a fuel cell stack that produces electricity by use of a fuel, a fuel cell cooler that cools cooling water for cooling the fuel cell stack through exchange of heat with external air, an exhaust line that exhausts an exhaust gas generated by the fuel cell stack, a condenser fluidically connected to the exhaust line to generate condensate by condensing the exhaust gas and store the generated condensate, an ejector connected to the condenser to eject the condensate to an external surface of the fuel cell cooler, and a condensate cooler connected to the condenser to cool the condensate stored in the condenser through exchange of heat therebetween.