A cooling control system and method for fuel cells are provided. The cooling control system includes a fuel cell, a cooling circulation line connected to the fuel cell to circulate cooling water for cooling the fuel cell therein and a cooling water pump provided on the cooling circulation line to adjust a circulation amount of the cooling water. A calculation unit calculates a thermal energy change of the fuel cell based on a heating value and an amount of radiant heat of the fuel cell. A controller operates the cooling water pump based on the calculated thermal energy change of the fuel cell.