Unmanned aerial vehicle technology is the most advanced and helpful in almost every area of interest in human work. These devices become autonomous and can fulfil a variety of tasks, from simple imaging and obtaining data to search and rescue operations. The most challenging environment for search and rescue operations is the mountainous area. This article is devoted to the theoretical description and simulation tests of a prototype method of landing the light and the medium-weight UAVs used as supplementary devices for SAR (search and rescue) and HEMS (helicopter emergency medical service) in hard-to-reach mountainous terrains. The autonomous flight of a UAV in mountainous terrain has many specifics, and it is usually performed according to predetermined map points (pins) uploaded directly into the control software of the UAV. It is necessary to characterise each point flown on the chosen flight route line in advance and therefore to know its exact geographical coordinates (longitude, latitude and height of the point above the terrain), and the control system of UAV must react to the change in the weather and other conditions in real time. Usually, it is difficult to make this forecast with sufficient time in advance, mainly when UAVs are used as supplementary devices for the needs of HEMS or MRS (mountain rescue service). The most challenging phase is the final approach and landing of the UAV, especially if a loss of GNSS (global navigation satellite system) signal occurs, like in the determined area of the Little Cold Valley in the Slovak High Tatras—which is infamous for the widespread loss of GNSS signals or communication/controlling connection between the UAV and the pilot-operator at the operational station. To solve the loss of guidance, a new method for guiding and controlling the UAV in its final approach and landing in a determined area is tested. An alternative landing navigation system for UAVs in a specific mountainous environment—the authors’ designed frequency Doppler landing system (FDLS)—is briefly described but thoroughly tested with the help of artificial intelligence. An estimation of dynamic stability is used based on the time recording of the current position of the UAV, with the help of a frequency-modulated or amplitude-modulated signal based on the author’s prototype of a precision landing system designed for mountainous terrain. This solution could overcome the problems of GNSS signal loss. The presented research primarily evaluates the success of the simulation flights for the supplementary UAV. The success of navigating the UAV to land in the mountainous environment at an exact landing point using the navigation signals from the FDLS was evaluated at more than 95%.