Full airframe flutter analysis of a transport aircraft with T-tail configuration is performed for two fuselage lengths in order to assess the effect of fuselage plug-in on the empennage flutter characteristics when developing the stretched variants of the baseline aircraft. To fulfill this purpose, aeroelastic model consisting of stiffness, mass, and aerodynamic model is constructed for full airframe to describe the modal characteristics and unsteady aerodynamic forces. Based on the model constructed, the data needed for flutter analysis such as generalized mass, stiffness and unsteady aerodynamic matrices are computed and extracted for each analysis condition using MSC/NASTRAN with in-house DMAP ALTER. The data extracted are then used as input for in-house flutter analysis software called pyFlutter developed in KARI based on Python language. Complex eigenvalue problem at each flight speed is solved to find flutter roots using PKS method implemented in pyFlutter. Flutter roots are analyzed and the coupling modes involved in each flutter root are identified. A detailed analysis results for flutter roots are presented, and the coupling between bending modes and twist modes is identified as major flutter mechanism for empennage. Finally, flutter analysis results for two fuselage lengths are investigated and the effect on the empennage flutter characteristics is evaluated.