A fuel cell cooling system may include a fuel cell module including a fuel cell stack, a cooling module that includes a cooling tower in which cooling fluid is accommodated and adjusts a temperature of the fuel cell module, a heat exchanger that exchanges heat between first circulation cooling water circulating in the fuel cell module and second circulation cooling water circulating in the cooling tower, and a condensate supply line connected to the cooling tower to supply, to the cooling tower, water generated in a power generation process of the fuel cell module.