The increasing demand for air traffic at airports necessitates the efficient utilization of ground facilities such as runways and taxiways. Intersecting departures, in which one or more aircraft take off from intersecting points on the runway, is a commonly used approach to increase runway capacity and reduce ground delays and taxi times, as well as noise and air pollution. However, the procedure carries potential risks such as runway incursion and excursion. This creates a trade-off between minimizing the number of intersecting departures and minimizing ground delays. In practice, the decision to perform an intersecting departure is ultimately up to the pilot, resulting in uncertainty in the acceptance rate of these types of takeoffs. In this study, a departure sequencing model was developed for a single-runway airport that considers intersecting departures and various pilot acceptance rate scenarios. The primary objective of the model is to minimize total ground delay, including taxi delays, runway holds, and conflict holds. The secondary objective is to minimize the number of intersecting departures by directing the most operationally critical aircraft to the intersection takeoff. The epsilon constraint method—a multi-objective scalarization method—was used to reveal the trade-offs between the objective functions. The results of the model were compared with a traditional scenario that only allows take offs from the beginning of the runway. As a result, average delay savings ranged from 17.1% to 31.5% in various acceptance rate scenarios, as well as average taxi time savings ranging from 4.9% to 8.4% compared with the traditional scenario.