Permeability is one of the fundamental properties of porous media and is required for largescale Darcian fluid flow and mass transport models. Whilst permeability can be measured directly at a range of scales, there are increasing opportunities to evaluate permeability from pore-scale fluid flow simulations. We introduce the free software Finite-Difference Method Stokes Solver (FDMSS) that solves Stokes equation using a finite-difference method (FDM) directly on voxelized 3D pore geometries (i.e. without meshing). Based on explicit convergence studies, validation on sphere packings with analytically known permeabilities, and comparison against lattice-Boltzmann and