In this paper, we present a novel intelligent control system for rat navigation based on video tracking and state machine techniques. And we demonstrate the automatic navigation of a rat to follow a preset course. The system consists of these components: (1) a wireless backpack stimulator comprised of stimulating circuit, control processor and bluetooth transceivers, (2) a video camera device capturing the rat?s movement, (3) a state machine based control program generating navigation commands automatically. The main contribution of this work is the intelligent control system for navigating a rat accurately and automatically in a comparatively narrow space. Experiment results show that the system is stable and practical.