Flutter suppression is an important aspect from aerospace structural stability point of view and therefore it has been an area of active research in aerospace industry. Flutter is a function of plunge and pitch motion, resulting in a two degree of freedom motion. If the dynamic stability is not achieved, it can lead to limit cycle oscillations which may further lead to structural failure. In this work, a quasi steady aerodynamic model is used and a robust controller based on Uncertainty and Disturbance Estimation (UDE) and Sliding Mode Control (SMC) is proposed for active flutter suppression. In UDE based Sliding Mode Controller design, flutter suppression is achieved by estimation and compensation of the effect of lumped uncertainties in the system. UDE design with first order filter is implemented and results are presented with a parametric uncertainty of 20 % in the system. It is shown that the proposed strategy has enhanced the performance of the closed loop system by 38 % beyond the critical flutter speed. Limitations of SMC scheme in terms of chattering phenomena and a priori knowledge of boundedness of disturbance are also mitigated in the proposed robust controller design. © 2016 IEEE.