An apparatus and a method for controlling a fuel electrode drain valve of a fuel cell system are disclosed. The apparatus includes: a hydrogen sensor that measures the concentration of hydrogen released by opening a fuel electrode drain valve, a first pressure sensor that measures the inlet pressure of the fuel electrode drain valve, a second pressure sensor that measures the outlet pressure of the fuel electrode drain valve; and a controller that controls the opening area of the fuel electrode drain valve to the maximum value when draining the condensate and controls the opening area of the fuel electrode drain valve based on the difference between the inlet pressure and the outlet pressure of the fuel electrode drain valve when purging the hydrogen.