The future revolution of the air traffic system imposes the development of a new class of Flight Management Systems (FMS), capable of providing the aircraft with real-time reference flight parameters, necessary to fly the aircraft through a predefined sequence of waypoints, while minimizing fuel consumption, noise and pollution emissions. The main goal is to guarantee safety operations while reducing the aircraft environmental impact, according to the main international research programs. This policy is expected to affect also the Unmanned Aerial Systems (UASs), as soon as they will be allowed to fly beyond the restricted portions of the aerospace where they are currently confined. In the future, in fact, UASs are expected to fly within the whole civilian airspace, under the same requirements deriving from the adoption of the Performance Based Navigation (PBN). For UASs, the most attractive strategy to reach this goal consists in adopting the mature technology developed for the civil aviation both in terms of operative functions and performance.The current literature lacks of examples dedicated to the control algorithms, which should operate the onboard autopilots and guide the aircraft through the reference calculated trajectory. This paper presents the implementation of a new generation FMS, composed by a trajectory optimization tool and a guidance and control algorithm, interfaced with a suite of proprietary Automatic Flight Control Systems (AFCSs). Different guidance and control algorithms for the FMS are presented and tested on a 6DOF nonlinear mathematical model of a civil aircraft (MASLab), developed within the Clean Sky research program.