An important component for any uninhabited aerial vehicle (UAV) to accomplish mission tasks, consisting of crossing several target points while overcoming obstacles along the flight path, is the trajectory management system. This paper presents new methodology for developing UAV trajectory management systems based on integrating flight path planning and generation functions along with trajectory guidance and attitude control functions, implemented with fuzzy logic principles during system design in order to make the UAV capable of accomplishing its mission, especially when damage or failure prevents usage of the primary lateral control input. A method for trajectory management system design in three-dimensional space without aileron capability is proposed and its implementation in a six degree of freedom nonlinear closed-loop flight dynamic system is presented. Examples of two-waypoint missions with stationary obstacles, using the proposed fuzzy logic based trajectory management system designed as a backup failure mode for the UAV, is presented. Simulation results demonstrate the potential of the proposed approach.