Effect of boundary stress on permeability in porous media at pore‐scale is investigated by means of numerical methods for computing deformation of rock material in the presence of pore fluid. We implement a partitioned, strongly coupled solver for transient fluid‐solid simulations with independent conformed interface meshes for the fluid and solid domains. Fluid flow and solid computations were performed using the finite element method. External load is prescribed along the solid boundary in gradual steps to examine the extent of pore‐scale deformation along internal grain walls while applying a fixed constraint at the opposite end to ensure uniform stress distribution across the media. Hydrodynamic interactions between the pore walls and the matrix leading to interface displacements by fluid viscous forces are also investigated by examining fluid flow with different combinations of Reynolds number. Coupling is achieved via traction and displacements boundary conditions at the interface with respect to Lagrangian coordinates. The role of particle shape in the matrix deformation process is also considered in this paper. In order to examine the how particle shape affects local affects local permeability/stress, we examine fluid movement based on varying Reynolds numbers in Berea sandstone obtained from Micro‐CT image scans at high resolution, and artificially constructed random polydisperse 3‐D sphere packs. It was found that permeability alteration under the influence of uniaxial stress was more in the sandstone sample than in the sphere‐pack and that the sphere‐pack deformed less than the actual sample due to pore geometry, surface smoothness, and homogeneity.