A three-dimensional inviscid flow solver has been developed based on unstructured meshes for the investigation of the effect of the external stores on the tail surfaces of a generic fighter aircraft. The numerical method is based on a vertex-centered finite-volume discretization and an implicit point Gauss-Seidel time integration. The calculations were made for a steady flow and the computed results were compared with experimental data to validate the flow solver. An unsteady time-accurate computation of the generic fighter aircraft with external stores at transonic flight conditions showed that the external stores cause unsteady loading on the horizontal tail surface due to the mutual interference between their wake and the horizontal tail surface. It was shown that downward deflection of the trailing edge flap significantly reduces the undesirable interference effect.