A simulation environment for the numerical calculation of permeation processes through human skin has been developed. In geometry models that represent the actual cell morphology of stratum corneum (SC) and deeper skin layers, the diffusive transport is simulated by a finite volume method. As reference elements for the corneocyte cells and lipid matrix, both three-dimensional tetrakaidecahedra and cuboids as well as two-dimensional brick-and-mortar models have been investigated. The central finding is that permeability and lag time of the different membranes can be represented in a closed form depending on model parameters and geometry. This allows a comparison of the models in terms of their barrier effectiveness at comparable cell sizes. The influence of the cell shape on the barrier properties has been numerically demonstrated and quantified. It is shown that tetrakaidecahedra in addition to an almost optimal surface-to-volume ratio also has a very favorable barrier-to-volume ratio. A simulation experiment was successfully validated with two representative test substances, the hydrophilic caffeine and the lipophilic flufenamic acid, which were applied in an aqueous vehicle with a constant dose. The input parameters for the simulation were determined in a companion study by experimental collaborators.