A system and method for controlling power of a fuel cell for a vehicle are provided. The method includes measuring a temperature of the fuel cell and when the measured temperature of the fuel cell is within a high temperature range in which a power threshold value of the fuel cell is reduced based on an increase in temperature of the fuel cell and when the measured temperature of the fuel cell is increased and then is equal to or greater than a predetermined temperature a power threshold value is reduced from a power value at the predetermined temperature. The high temperature range is a range between a third temperature at which the power threshold value starts to be reduced based on the increase in temperature of the fuel cell and a fourth temperature at which the power threshold value is reduced and then reaches the minimum power threshold value.