This paper presents the modeling of a novel pressure control mechanism for a common rail (CR) fuel injection system of internal combustion engines (ICE). The pressure fluctuations in the common rail caused by multiple injections negatively affect the accuracy of both injected fuel quantities and flow rates. The objective of this work is to design a new control mechanism to suppress the pressure pulsation in the rail. First we develop a one-dimensional distributed model for the common rail by using basic fluid flow equations, which can capture the distributed dynamics of the pressure disturbances in the rail and this result is validated with a physics based simulation model in AMESIM®. The periodic nature of injection event due to stroke by stroke motion of the ICE generates disturbance in the rail which in the rotational angle domain presents a primarily periodic signal. However, the period changes in the time domain due to the variation in engine speed. We then propose the concept of an active fluid storage device like a piezoelectric actuator (PZT) to minimize this pressure fluctuations. The location of the actuator on the common rail has also been evaluated to maximize its effect. Finally a time-varying repetitive controller is designed to compensate for the periodic pressure disturbances in the rotational angle domain.