In the present era of aviation technology, autonomous navigation and control have emerged as a prime area of active research. Owing to the tremendous developments in the field, autonomous controls have led today’s engineers to claim that future of aerospace vehicle is unmanned. Development of guidance and navigation algorithms for an unmanned aerial vehicle (UAV) is an extremely challenging task, which requires efforts to meet strict, and at times, conflicting goals of guidance and control. In this paper, aircraft altitude and heading controllers and an efficient algorithm for self-governing navigation using MATLAB® mapping toolbox is presented which also enables loitering of a fixed wing UAV over a specified area. For this purpose, a nonlinear mathematical model of a UAV is used. The nonlinear model is linearized around a stable trim point and decoupled for controller design. The linear controllers are tested on the nonlinear aircraft model and navigation algorithm is subsequently developed for for autonomous flight of the UAV. The results are presented for trajectory controllers and waypoint based navigation. Our investigation reveals that MATLAB® mapping toolbox can be exploited to successfully deliver an efficient algorithm for autonomous aerial navigation for a UAV.