In this paper, we develope the navigation system for patrol robots in indoor environment. The proposed system consists of PDA map modelling, a localization algorithm based on a global position sensor and an automatic charging station. For the practical use in security system, the PDA is used to build object map on the given indoor map. And the builded map is downloaded to the mobile robot and used in path planning. The global path planning is performed with a localization sensor and the downloaded map. As a main controller, we use PXA270 based hardware platform in which embedded linux 2.6 is developed. Data handling for various sensors and the localization algorithm are performed in the linux platform. Also, we implemented a local path planning algorithm for object avoidance with ultra sonar sensors. Finally, for the automatic charging, we use an infrared ray system and develop a docking algorithm. The navigation system is experimented with the two-wheeled mobile robot using North-Star localization system.