Modern aircrafts require improved performance and maneuverability while they conduct the missions. The flutter, an aeroelastic phenomenon is one of the important situations that limit the aircraft speed. Furthermore, for aircraft operated at high speed, many uncertainties may exist in its structural and aerodynamics characteristics. Especially, a slight change in the wing structural mode may induce a variation in its aerodynamic force distribution. In this work, an interval-based approach is used to handle the uncertainties associated with the flutter analysis. The set-theoretic representation of uncertainty is motivated by a possible lack of detailed probabilistic information on the distributions of the parameters. The analysis procedure is performed on an aircraft wing structure using finite element idealization and the results have shown the effectiveness and feasibility of the interval method. The order of the aerodynamic, mass and stiffness matrices of the assembled structures is reduced by introducing the first few natural modes of the structure as generalized coordinates. System equivalent reduction expansion process is used for model reduction which uses the generalized inverse and carries information pertaining to the selected modes at the selected set of degrees of freedoms. The system equivalent reduction formulation allows the reduction process to preserve the dynamics of the full system in a reduced set of matrices. Thus the order of the eigenvalue problem in the flutter analysis is reduced to one-third of the corresponding statics problem.