Sulfuric acid cross-linked chitosan membranes filled with a different amount of magnetite, were prepared. The permeation behavior of ethanol and water vapors in vapor permeation experiments were studied. Permeation rates were measured. Mass transport coefficients were evaluated. The study has been carried out to determine the influence of magnetic powder dispersed inside of the chitosan membrane on ethanol-water separation. The diffusion, fluxes, and permeation coefficients increased with greater amount of magnetite content. The separation factor increased with increasing flux and the best results were achieved for the membrane containing 15% w/w magnetite. The research allows optimizing the preparation procedure of chitosan magnetic membranes cross-linked by sulfuric acid with the best permeation properties.