In this study, structural vibration analyses of a smart unmanned aerial vehicle (UAV) have been conducted considering dynamic loads generated by rotating rotor and wakes. The present UAV (TR-S5-03) finite element model is constructed as a full three-dimensional configuration with different fuel conditions and tilting angles for helicopter, transition and airplane flight modes. Practical computational procedure for modal transient response analysis (MTRA) is established using general purpose finite element method (FEM) and computational fluid dynamics (CFD) technique. The dynamic loads generated by rotating blades in the transient and forward flight conditions are calculated by unsteady CFD technique with sliding mesh concept. As the results of present study, transient structural displacements and accelerations are presented in detail. In addition, vibration characteristics of structural parts and installed equipments are investigated for different fuel conditions and tilting angles.