A method and an apparatus for controlling the operation of a fuel cell system. The method can include, actively controlling the fuel cell system without a fuel concentration sensor by: measuring an output voltage, an output current, and a temperature of a fuel cell stack; obtaining a first fuel feeding amount corresponding to the measured output values; comparing a reference temperature corresponding to the measured output values with the measured temperature; and obtaining a second fuel feeding amount by compensating the first fuel feeding amount with a value corresponding to difference between the reference temperature and the measured temperature.