In this research, the effect of rail vehicle carbody’s flexural modes on the ride comfort of an example high-speed railway vehicle is investigated. The vehicle is modeled as a rigid multi-body system, where the rigid body vertical, longitudinal, pitch, and roll degrees of freedom of the carbody and bogie frames and the rigid body vertical and roll degrees of freedom of the wheelsets are considered. An Euler–Bernoulli beam theory is used to account for the flexural motion of the carbody. The longitudinal interaction between carbody and bogie through the traction rod is modeled as a nonlinear spring element. The corresponding equations of motion of the system in the frequency domain are obtained by using the equivalent linearization method. The effect of the traction rod is explored by using this model. Also, the optimal stiffness of the traction rod element that minimizes the flexural vibrations of the carbody is obtained through a genetic algorithm. With the optimal stiffness for the traction rod, the ride quality index at the center of the carbody floor is improved by 41% at a speed of 300 km/h. For the validation of numerical results, a scaled model of the vehicle with a scale factor of 24.5 was constructed, and its associated results are presented. The model was excited by random input signals, which were generated based on the power spectral density of the track irregularity function. The agreement between the simulation results and the scaled experimental outcome when compared with the measured data from other sources is found to be satisfactory. In the framework of the physical scaled model, the filtering effect due to the vehicle bogie base is also examined.