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Common rail based direct injection system is critical for improving the fuel economy and emissions of both gasoline and diesel engines. The fuel pressure pulsation inside the common rail is induced by high-speed flows in and out of the common rail. This phenomenon could adversely affect the accuracy of injected fuel quantities and flow rates. So it is desirable to compensate for the pressure pulsations in a high pressure fuel injection system. Due to the stroke by stroke motion of the internal combustion engine, the fuel pressure pulsation is primarily periodic with respect to the engine rotational-angle since fuel injection timing is scheduled on an angular basis. However, the period of the pressure pulsation changes in time domain as the rotational speed varies in general. To compensate for the pressure pulsations, current control practice is to throttle the fuel through an electro-hydraulic valve, which not only results in energy loss but also has limited effect due to the bandwidth of the valve and the control. In this paper, we apply recently developed time-varying internal model-based design to compensate for the time-varying but angle dependent pressure pulsations.