The main objective of this study is analysis of dispersive mixing inside a batch electrophoretic cell due to Joule heating, especially for the case of non-Newtonian carriers. To this end, a carrier fluid that follows the Eyring rheological model is used in the analysis of the species convective-diffusive equation that describes the solute motion inside the device. The hydrodynamic problem (Bosse, M. A. et al., Electrophoresis 2002, 23, 2149-2156) of the electrophoretic cell is sequentially coupled to this equation. Then, by following a procedure based on the area-averaging method, an effective diffusion coefficient is obtained. This equation is the first a priori design equation for devices such as the ones analyzed in this contribution. It is useful in determining mixing conditions for the values of the relevant parameters of the physical system. The results of this analysis are used to study the cell behavior under several conditions imposed by their main parameters. Finally, some suggestions are offered about the use of Eyring fluids as potential carriers useful for controlling dispersive mixing in batch electrophoretic cells.