A Hybrid Optimal Control (HOC) framework which can be used in conjunction with existing optimal control software is presented. By using hybrid optimal control theory, trajectory optimization problems for systems that are both discrete time and continuous time from a mathematical perspective can be solved. A case study on multi-aircraft formation flying for civil aviation is performed which demonstrates the capabilities of the designed method. Whilst previous research has dealt with either high accuracy trajectories for small formation flying problems or low accuracy modelling of very large formation flying trajectories, in this thesis HOC is used to achieve a high accuracy optimal trajectory for formations of three aircraft and larger. Given the number of flights that are performed every day, the impact of saving fuel just by optimizing their trajectories using formation flying can be significant on a global scale, both environmentally and economically.