Flutter is a destructive and potentially explosive phenomenon that is the result of the simultaneous interaction of aerodynamic, elastic, and inertial forces. The nature of flutter mandates that flutter flight testing be cautious and conservative. Because of this, further investigation of uncertainty analysis with respect to the flutter problem is desired and warranted. Prediction of flutter in the transonic regime requires computationally expensive high-fidelity simulation models. Because of the computational demands, traditional uncertainty analysis is not often applied to transonic flutter prediction, resulting in reduced confidence in the results. The work described herein is aimed at exploring various methods to reduce the existing computational time limitations of traditional uncertainty analysis. Specifically, the coupling of design of experiment and response surface methods and the application of analysis are applied to a validated aeroelastic model of the AGARD 445.6 wing. From a high-fidelity nonlinear aeroelastic model, a linear reduced-order model is produced that captures the essential dynamic characteristics. Using reduced-order models, the design of experiment, response surface methods, and -analysis approaches are compared with traditional Monte Carlo-based stochastic simulation. All of these approaches to uncertainty analysis have advantages and drawbacks. Results from these methods and their robustness are compared and evaluated.