An apparatus and method for controlling a fuel injection system of an internal combustion engine is disclosed. Each fuel injector in the system is operated to perform a predetermined injection pattern per engine cycle. A signal representative of a fuel pressure within the fuel rail during the operation of the fuel injectors is sampled. A Fourier analysis of the fuel rail pressure signal is performed to determine one or more harmonic components thereof. The determined harmonic components of the fuel rail pressure signal are used to calculate a dynamic fuel quantity that flows through a fuel injector during an injection pulse of the injection pattern. A fuel quantity actually injected by the fuel injector during the injection pulse as a function of the dynamic fuel quantity is calculated.