Disclosed are a method and a system for controlling an output current of a fuel cell stack. The method of controlling the output current of the fuel cell stack, whereby the output current is controlled by using a data map configured with a limited output current according to a temperature of a fuel cell coolant, includes: deriving an average cell voltage value and a minimum cell voltage value of a plurality of cells constituting the fuel cell stack; correcting the data map by using the derived average cell voltage value and the derived minimum cell voltage value; and limiting the output current of the fuel cell according to the corrected data map.