This study addresses the modeling of transdermal diffusion of drugs to better understand the permeation of molecules through the skin, especially the stratum corneum, which forms the main permeation barrier to percutaneous permeation. In order to ensure reproducibility and predictability of drug permeation through the skin and into the body, a quantitative understanding of the permeation barrier properties of the stratum corneum (SC) is crucial. We propose a multiscale framework of modeling the multicomponent transdermal diffusion of molecules. The problem is divided into subproblems of increasing length scale: microscopic, mesoscopic, and macroscopic. First, the microscopic diffusion coefficient in the lipid bilayers of the SC is found through molecular dynamics (MD) simulations. Then, a homogenization procedure is performed over a model unit cell of the heterogeneous SC, resulting in effective diffusion parameters. These effective parameters are the macroscopic diffusion coefficients for the homogeneous medium that is “equivalent” to the heterogeneous SC, and thus can be used in finite element simulations of the macroscopic diffusion process. The resulting drug flux through the skin shows very reasonable agreement to experimental data.