This paper presents the modeling and analysis of the pressure distribution and lifting force generated by a Bernoulli gripper when handling flexible substrates such as thin silicon wafers. A Bernoulli gripper is essentially a radial airflow nozzle used to handle large and small, rigid and nonrigid materials by creating a low pressure region or vacuum between the gripper and material. Previous studies on Bernoulli gripping have analyzed the pressure distribution and lifting force for handling thick substrates that undergo negligible deformation. Since the lifting force produced by the gripper is a function of the gap between the handled object and the gripper, any deformation of the substrate will influence the gap and consequently the pressure distribution and lifting force. In this paper, the effect of substrate (thin silicon wafer) flexibility on the equilibrium wafer deformation, radial pressure distribution and lifting force is modeled and analyzed using a combination of computational fluid dynamics (CFD) modeling and finite element analysis. The equilibrium wafer deformation for different air flow rates is compared with experimental data and is shown to be in good agreement. In addition, the effect of wafer deformation on the pressure and lifting force are shown to be significant at higher volumetric airflow rates. The modeling and analysis approach presented in this paper is particularly useful for evaluating the effect of gripper variables on the handling stresses generated in thin silicon wafers and for gripper design optimization.