A finite element model was developed and updated using experimental data for a composite flying-wing aircraft named mAEWing1, a small-scale replica of X-56 type aircraft. This flying-wing composite aircraft was fabricated at the University of Minnesota and subsequently tested for its aeroelastic behavior. The finite element model was developed in NASTRAN using different approaches to determine the cross section stiffness and mass properties. One method to obtain the model is to use the equivalent stiffness and mass properties for the beam, which are obtained from a static test. Another method uses the developed cross-sectional analysis tool for accurate stiffness and mass properties for mAEWing1 wing. A three-step subcomponent-based optimization approach is considered to update the mass and stiffness distributions for use in the finite element model. Steps I and II update the mass distribution for the center-body and the individual wing of the aircraft, respectively, to match the test article’s mass properties. The individual wing stiffness distribution can be also updated in Step II by using the available individual wing GVT mode results. The updated finite element models for the center-body and the wing were then assembled as the initial finite element model for the full aircraft model, in Step III. This initial finite element model was then updated to match both the test article’s mass properties and the GVT modal results for the full aircraft model. The mass properties for both the individual wing and the center-body obtained from the full aircraft finite element model updating in Step III are then compared against the test data. Once the difference between the mass properties for the updated finite element models and the available test data is less than a given allowance criteria, the program is terminated and a near best finite element model is output.