Thin-walled beams are increasingly used in light engineering structures. They are economical, easy to manufacture and to install, and their load capacity-to-weight ratio is very favorable. However, their walls are prone to local buckling, which leads to a reduction of compressive, as well as flexural and torsional, stiffness. Such imperfections can be included in such components in various ways, e.g., by reducing the cross-sectional area. This article presents a method based on the numerical homogenization of a thin-walled beam model that includes geometric imperfections. The homogenization procedure uses a numerical 3D model of a selected piece of a thin-walled beam section, the so-called representative volume element (RVE). Although the model is based on the finite element method (FEM), no formal analysis is performed. The FE model is only used to build the full stiffness matrix of the model with geometric imperfections. The stiffness matrix is then condensed to the outer nodes of the RVE, and the effective stiffness of the cross-section is calculated by using the principle of the elastic equilibrium of the strain energy. It is clear from the conducted analyses that the introduced imperfections cause the decreases in the calculated stiffnesses in comparison to the model without imperfections.