Abstract-This paper presents real-time MRI-based control of a ferromagnetic microcapsule for endovascular navigation. The concept was studied for future development of microdevices designed to perform minimally invasive interventions in remote sites accessible through the human cardiovascular system. A system software architecture is presented illustrating the different software modules to allow 3D navigation of a microdevice in blood vessels, namely: (i) vessel path planner, (ii) magnetic gradient steering, (iii) tracking and (iv) closed-loop navigation control. First, the position recognition of the microrobot into the blood vessel is extracted using Frangi vesselness filtering from the pre-operation images (3D MRI imaging). Then, a set of minimal trajectory is predefined, using Fast Marching Method (FMM), to guide the microrobot from the injection point to the tumor area through the anarchic vessel network. Based on the pre-computed path, a Generalized Predictive Controller (GPC) is proposed for robust time-multiplexed navigation along a 2D path in presence of pulsative flow. The simulation results suggest the validation of the proposed image processing and control algorithms. A series of disturbances introduced in the presence and absence of closed-loop control affirms the robustness and effectiveness of this predictive control system.