Schedule design in the transportation and logistics sector is a widely studied problem. Transport service providers, such as the train industry and aviation, aim for schedules to be on-time according to the planning (i.e., on-time performance or OTP) in order to increase the service level by ensuring that passengers actually make their connections and to reduce costs. Transportation services also aim for schedules that serve a high variety of destinations and frequency of connections (i.e., connectivity). OTP and connectivity are both highly dependent on buffer time: more lucrative connections can often be offered by reducing the buffer time in the schedule, while more delay can be absorbed by more buffer time. Given strict constraints on the minimum turnaround time of aircraft and minimum (and maximum acceptable) transfer times of passengers, assigning buffer time in an already tightly planned schedule to optimize OTP and connectivity simultaneously is a big challenge. This research presents a novel multi-objective formulation of a daily flight schedule where buffer scheduling is used to ensure the optimal balance between OTP of the schedule and the passenger connections as connectivity, given the tight restrictions. This problem formulation is solved using a simulation–optimization framework. Specifically, we use the Multi-Objective Evolutionary Algorithm (MOEA) BORG. As a proof of concept, a daily European flight schedule of a large international airline is optimized on both OTP and connectivity. The results demonstrate that the presented multi-objective formulation and associated solving through simulation–optimization can result in candidate schedules with both better on-time performance and a higher connectivity.