Transonic flutter analyses are performed for a three-dimensional wing based on the use of the TSD3KR finite difference code. The TSD3KR code has been originally developed for the analysis of transonic unsteady aerodynamics and aeroelastic stability. The present TSD3KR code has many advantages in the transonic flutter calculations because of simple grid generation and very fast computation. In this study, aerodynamic characteristics for the various wings are presented to validate current analysis program. Transonic aeroelastic flutter boundaries of 56° leading-edge swept-back wing computed by TSD3KR, DLM and DPM codes are compared at various free stream Mach numbers. The present aerodynamic and flutter calculation results calculated by the current TSD3KR code show very good agreement with the experimental data and previous computation results. However, DLM and DPM codes do not predict the transonic dip near Mach number 1 because of its theoretical limitation.