A new robust numerical technique was proposed for analyzing chloride transient diffusion in concrete with non-homogenous coefficient. The method was based on a meshless boundary element method which results in an integral equation for explicitly evaluating field chloride quantities. Weighted residual method and Green’s function were adopted to derive domain and boundary integral equations. A radial integration method coupling with radial basis function approximation technology was used to convert domain integral into equivalent boundary integral. With central finite difference method, an explicit time iteration scheme was established for solving transient diffusion equation. Two numerical examples for 2D diffusion problem were given to demonstrate the robustness of the proposed method. Numerical results show that the non-homogenous diffusion coefficient causes the chloride distribution non-uniform, and the diffusion process is nonlinear with respect to time.