This contribution is devoted to analyzing and to implementing a discrete time fractional order structure for a PI regulator. A loop shaping problem is formulated as a part of this approach in terms of a Min-Max optimisation problem in which a combination of a flatness based control together with a PI regulator is included into the control strategy. The system which is examined uses an actuator with permanent magnets for controlling the intake valve engine. The specifications on the control loop are guaranteed by means of a fractional PI regulator. This contribution underlines advantages of use of a fractional approach to design a PI controller. The effectiveness of the proposed application is proved by the simulation analysis. A comparison between the proposed fractional PI approach combined with a constrained Min-Max optimisation problem and an integer PI tuned with the same Min-Max optimisation problem structure is shown.