Wireless capsule endoscope (WCE) is a new diagnostic device that can be utilised for evaluating the whole digestive tract if effectively actuated. In this research, a new one degree of freedom (1DOF) actuation system based on a magnetic levitation concept is proposed for the capsule endoscope navigation system. The proposed system is used to move a permanent magnet inserted in WCE body by an arrangement of the current controlled electromagnetic actuator placed on a 3DOF movable frame. The aim of this study is to design a proportional–integral–derivative (PID) controller to suspend the capsule and keep it at a demand test region. DC and AC magnetic field-based positioning systems using the Hall effect sensor and the coil sensor, respectively are used to provide the controller by capsule position feedback. Improvement of the position feedback accuracy based on AC magnetic field using discrete Fourier transform is presented. Realistic simulation design of the system is implemented using Matlab/Simulink environment to validate the PID controller. The navigation scheme is implemented practically utilszing digital signal processor to verify the effectiveness of the controller. Finally, simulation and experimental results of the capsule navigation system are presented to show the performance of the proposed controller.