Wireless capsule endoscopes (WCE) are a new technology for inspection of the intestines, which offer many advantages over conventional endoscopes, while devices currently in use are passive and can only follow the natural transit of the intestines. There is a considerable interest in methods of controlled actuation for these devices. In this paper, an actuation system based on magnetic levitation is proposed, utilizing a small permanent magnet within the capsule and an arrangement of digitally controlled electromagnet placed on a movable frame. The objective of this paper is to design a multi-input multi-output (MIMO), three degrees-of-freedom (3DOF) tracking system for capsule endoscope. Two techniques, entire eigenstructure assignment (EEA) and linear quadratic regulator (LQR), are presented to design the controller of the system. The performance of the EEA and LQR controllers was compared based on the stability parameters to validate the proposed actuation system. Finally, simulation results suggest that the LQR approach can be used to synthesize a suitable and simple controller for this application.