In this study, the deformation and stress distribution of printed circuit board (PCB) with different thickness and composite materials under a shock loading were analyzed by the finite element analysis. The standard 8-layer PCB subjected to a shock loading 1500 g was evaluated first. Moreover, the finite element models of the PCB with different thickness by stacking various number of layers were discussed. In addition to changing thickness, the core material of PCB was replaced from woven E-glass/epoxy to woven carbon fiber/epoxy for structural enhancement. The non-linear material property of copper foil was considered in the analysis. The results indicated that a thicker PCB has lower stress in the copper foil in PCBs under the shock loading. The stress difference between the thicker PCB (2.6 mm) and thinner PCB (0.6 mm) is around 5%. Using woven carbon fiber/epoxy as core material could lower the stress of copper foil around 6.6% under the shock loading 1500 g for the PCB with 0.6 mm thickness. On the other hand, the stress level is under the failure strength of PCBs with carbon fiber/epoxy core layers and thickness 2.6 mm when the peak acceleration changes from 1500 g to 5000 g. This study could provide a reference for the design and proper applications of the PCB with different thickness and composite materials.