The model-based flight control system design for a highly flexible flutter demonstrator, developed in the European FLEXOP project, is presented. The flight control system includes a baseline controller to operate the aircraft fully autonomously and a flutter suppression controller to stabilize the unstable aeroelastic modes and extend the aircraft’s operational range. The baseline control system features a classical cascade flight control structure with scheduled control loops to augment the lateral and longitudinal axis of the aircraft. The flutter suppression controller uses an advanced blending technique to blend the flutter relevant sensor and actuator signals. These blends decouple the unstable modes and individually control them by scheduled single loop controllers. For the tuning of the free parameters in the defined controller structures, a model-based approach solving multi-objective, non-linear optimization problems is used. The developed control system, including baseline and flutter control algorithms, is verified in an extensive simulation campaign using a high fidelity simulator. The simulator is embedded in MATLAB and a features non-linear model of the aircraft dynamics itself and detailed sensor and actuator descriptions.