In this study, the structural damage and external store effects on the transonic flutter stability of a fighter type aircraft are investigated. As the damage area, the control surface-supporting structure has been selected because it is expected to affect the flutter stability sensitively. The transonic small disturbance (TSD) method is used for the analysis of unsteady aerodynamics because it is much faster than other computational fluid dynamics (CFD) schemes and is reliable for considering the control surface motions. The flutter analysis results are also compared with the results using a linear flutter analysis program to demonstrate the reliability of the analysis. This research shows that the flutter stability in the transonic regime can be further reduced after external stores are installed. This study also shows that although there is no significant decrease of flutter stability due to structural damage in subsonic regime, the flutter stability can be seriously deteriorated in the transonic regime at a certain level of damage. The effects of structural damage on the flutter stability should be carefully examined during the development of aircraft especially transonic regime.