Abstract Flutter in aeronautical panels is a type of self-excited oscillation which can occur during supersonic flights. At the flutter point the vibrations of the panel become unstable and increase significantly in time. This manuscript presents a semi-analytical model taking into account the stiffener’s base effects, in order to predict the aeroelastic response of laminated composite stiffened panels under supersonic flow. Krumhaar’s modified supersonic piston theory, which considers the radius effect, is adopted to model the aerodynamic loading. The proposed model has been validated against results available in the literature for various configurations. A parametric study considering different panels and stiffener configurations is also presented. The numerical results indicate that the stiffener base significantly affects the panel aeroelastic behavior. Preliminary studies also indicate that redistributing the laminate plies from the stiffener’s flange to its base significantly increases the torsion stiffness of the panel locally, opening new design possibilities that may lead to higher critical flutter speeds and therefore to better designs. The results also indicate that designs with plies distributed on the base may lead to a better flutter performance when the airflow is transverse to the longitudinal stiffener direction.