An apparatus for controlling a fuel cell of an environment-friendly vehicle, a system including the same, and a method thereof are provided. The apparatus includes a storage storing information mapping an amount of additional output of a fuel cell according to air density and a current battery state of a high voltage battery depending on a drive mode and a processor that controls an amount of output of the fuel cell in response to a required amount of output of a motor, the amount of output of the fuel cell being varied according to the air density, the current battery state, and the drive mode based on the information mapping the amount of additional output.