The growing interest in the development of hypersonic vehicles, driven by both civil and military applications, imposes significant challenges due to the nonlinear coupling between aerodynamic performance, propulsive behavior, structural integrity, and thermal effects. This work developed an integrated model of a waverider-type hypersonic vehicle, designated LOGAN (Large Over-Mach Glider Aircraft New-generation), fully coupling the six-degree-of-freedom flight dynamics with a transient thermodynamic scramjet engine model. The thermodynamic model, based on a one-dimensional formulation, represents in real time the processes of external and internal compression, supersonic combustion, and expansion, enabling the calculation of pressure, temperature, density, thrust, fuel consumption, and performance metrics directly as functions of flight conditions. The aerodynamic forces and moments were obtained from a nonlinear aerodynamic database dependent on Mach number, angle of attack, and control surface deflections, allowing the capture of characteristic hypersonic flight phenomena such as strong shock-wave interactions and boundary layer effects. The implemented control architecture included inner loops for attitude stabilization and outer loops for trajectory control. The performance analyses showed a strong sensitivity of the scramjet to variations in combustor efficiency, altitude, and Mach number, with higher specific impulses at elevated altitudes, but with penalties in propulsive efficiency and a relative increase in irreversibilities. Simulations under different load cases and flight conditions revealed that heavier configurations require higher angles of attack and greater fuel consumption, resulting in lower thermal and exergetic efficiency, while lighter configurations presented faster responses and better energy utilization. The controller evaluation demonstrated robustness in stabilization and trajectory tracking, although aerodynamic and dynamic pressure constraints imposed limitations under low Mach number and high-load conditions. Finally, the integration of the model with the FlightGear simulator enabled real-time simulation with three-dimensional visualization of trajectory and flight parameters, supporting model validation and control law tuning. The results obtained confirm the feasibility and relevance of the proposed approach for hypersonic vehicle analysis, providing a foundation for the design and optimization of future waverider configurations with scramjet propulsion.