A minimization of disturbance caused by aircraft noise events and a reduction of fuel consumption during the initial and final phase of flight. These are the two objectives that play an important role in the Flexible Runway Allocation Model. By taking into account fuel consumption alongside noise annoyance, this model enables to analyze and optimize runway allocation from a broader perspective. This study aims to identify the improvements that can be made with respect to the initial Flexible Runway Use Model. Accordingly, these enhancements should be implemented and quantified in order to establish the Improved Flexible Runway Allocation Model. The improvements that are found in this study relate to both objectives in the mixed integer linear programming optimization as well as particular linear constraints. A major contribution is made to the runway occupancy constraint, which has shown a transition from a single aircraft computational method to a pairwise flight separation approach based on RECAT-EU. The proposed Improved Flexible Runway Allocation Model is applied to a case study that represents daily operations at London Heathrow Airport. This model shows that, by assigning a small delay to inbound and/or outbound flights, significant contributions can be made with respect to noise annoyance in the vicinity of the airport as well as the overall fuel consumption from the airline’s perspective. By allowing opposite direction operations, flexibility is added to the use of the airport’s runway ends, which results in a more efficient utilization of the available capacity. The results of this analysis are visualized by means of a Pareto front, indicating the Pareto optimal solutions to a runway allocation assignment based on a differentiation in objective weights.