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A key feature of trajectory based operations (TBO) – a new concept developed to modernize the air traffic system – is the inclusion of preferences and priorities of the air traffic management (ATM) stakeholders. In this paper, we present a new mathematical model to optimize flights’ 4D-trajectories. This is a multi-objective binary integer programming (IP) model, which assigns a 4D-trajectory to each flight, while explicitly modeling priorities and highlighting the trade off involved with the Airspace Users (AUs) preferences. The scope of the model (to be used at pre-tactical level) is the computation of optimal 4D pre-departure trajectory for each flight to be shared or negotiated with other stakeholders and subsequently managed throughout the flight. These trajectories are obtained by minimising the deviation (delay and re-routing) from the original preferred 4D-trajectories as well as minimizing the air navigation service (ANS) charges subject to the constraints of the system. Computational results for the model are presented, which show that the proposed model has the ability to identify trade-offs between the objectives of the stakeholders of the ATM system under the TBO concept. This can therefore provide the ATM stakeholders with useful decision tools to choose a trajectory for each flight.