Electric vehicle battery enclosure systems under vibrational loading may experience structural damage, reducing the lifespan of lithium-ion cells. Honeycomb sandwich structures are widely used in EV battery systems due to their high stiffness-to-weight ratio and superior vibration performance. The present study is undertaken to investigate the dynamic behaviour of honeycomb sandwich panels using ANSYS Workbench. A three-dimensional model of a sandwich structure consisting of an aluminium core and composite face sheets is developed in ANSYS. Modal analysis and power spectral density-based random vibration analysis are performed to examine the impact of face-sheet thickness (0.5–2.5 mm) and layup configuration on structural performance. The modal analysis reveals that the natural frequencies increase considerably with thickness up to 1.5 mm due to increased bending stiffness. The results of random vibration analysis demonstrate a substantial reduction in total deformation and equivalent stress with increasing thickness. Among the configurations studied, the [0C/0G]/Core/[0G/0C] layup demonstrates the most favourable response under the present PSD loading condition due to fibre alignment with the principal loading direction. The findings are further converted into practical design guidelines for electric vehicle battery enclosures, including an appropriate face-sheet thickness range of 1.0–1.5 mm and fibre orientations aligned with the principal loading direction, while considering the associated mass penalty. These findings provide a design-oriented framework for selecting thickness and layup configuration to achieve a practical balance between vibration resistance and weight.