This article presents an energy-efficient method of controlling unmanned aircraft (fixed-wing UAVs), which consists of three groups of algorithms: aerial vehicle route planning, in-flight control, and algorithms to correct the preplanned flight trajectory. All algorithms shall take into account the existence of obstacles that the UAV must avoid and wind gusts in the UAV’s area of operation. Tests were carried out on the basis of the UAV mathematical model, stabilization and navigation algorithms, and Dryden turbulence model, considering the parameters of the UAV’s propulsion system. The work includes a detailed description of constructing a network of connection that is used to plan a UAV mission. It presents the algorithm for determining the actual distances between the different points in the field of action, which takes into account the existence of obstacles. The algorithm shall be based on methods for determining the flight trajectory on a hexagonal grid. It presents the developed proprietary UAV path planning algorithm based on a model from a group of algorithms of mixed integer linear problem (MILP) optimization. It presents the manner in which the pre-prepared flight path was used by UAV controllers that supervised the flight along the preset path. It details the architecture of contemporary unmanned aerial vehicles, which have embedded capability to realize autonomous missions, which require the integration of UAV systems into the route planning algorithms set out in the article. Particular attention has been paid to the planning and implementation methods of UAV missions under conditions where wind gusts are present, which support the determination of UAV flight routes to minimize the vehicle’s energy consumption. The models developed were tested within a computer architecture based on ARM processors using the hardware-in-the-loop (HIL) technique, which is commonly used to control unmanned vehicles. The presented solution makes use of two computers: FCC (flight control computer) based on a real-time operating system (RTOS) and MC (mission computer) based on Linux and integrated with the Robot Operating System (ROS). A new contribution of this work is the integration of planning and monitoring methods for the implementation of missions aimed at minimizing energy consumption of the vehicle, taking into account wind conditions.