The use of fuel cell (FC) stacks in commercial vehicles imposes significant demands on their safety and reliability. In this context the impact of mechanical vibrations on stack level has received limited research attention. In this study, the mechanical and vibrational characteristics of a FC stack are investigated using a combined experimental and numerical approach. A homogenized cell model was developed to simplify finite element analyses and significantly reducing computational time while maintaining a high level of accuracy. A multiscale optimization strategy was employed to calibrate the model parameters against experimental data obtained from free-free modal analysis and shaker tests, enhancing accuracy in predicting the stack’s response to mechanical loads. In addition, due to the lack of specific mechanical testing protocols for commercial fuel cell vehicles, a mechanical vibration test based on ISO 12405 was employed to assess the influences of mechanical stress testing on the stack. Structural imaging using X-ray computed tomography (CT) was conducted to evaluate the global structural changes of the stack after 21 hours of testing time. The analysis revealed permanent displacements of the bipolar plates and threaded rods, indicating the impact of mechanical stress on the stack’s structural integrity. The findings underscore the complex behavior of the FC stack under mechanical loads and highlight the necessity for systematic structural analyses to improve the durability and reliability of fuel cell systems in mobile applications.