The aim of this paper is to present a flutter analysis of a 3D Box-Wing Aircraft (BWA) configuration. The box wing structure is considered as consisting of two wings (front and rear wings) connected with a winglet. Plunge and pitch motions are considered for each wing and the winglet is modeled by a longitudinal spring. In order to exert the effect of the wing-joint interactions (bending and torsion coupling), two ends of the spring are located on the gravity centers of the wings tip sections. Wagner unsteady model is used to simulate the aerodynamic force and moment on the wing. The governing equations are extracted via Hamilton's variational principle. To transform the resulting partial integro-differential governing equations into a set of ordinary differential equations, the assumed modes method is utilized. In order to confirm the aerodynamic model, the flutter results of a clean wing are compared and validated with the previously published results. Also, for the validation, the 3D box wing aircraft configuration flutter results are compared with MSC NASTRAN software and good agreement is observed. The effects of design parameters such as the winglet tension stiffness, the wing sweep and dihedral angles, and the aircraft altitude on the flutter velocity and frequency are investigated. The results reveal that physical and geometrical properties of the front and rear wings and also the winglet design have a significant influence on BWA aeroelastic stability boundary.