The method of the present invention for separating and purifying a cationic protein is performed by using an electrodialysis apparatus. The electrodialysis apparatus used herein includes an electrodialysis bath having an anode and a cathode. The electrodialysis bath includes an anode compartment, a raw material loading compartment, a concentration compartment, and a cathode compartment in this order from the anode side. The anode compartment and the raw material loading compartment are divided from each other by a porous membrane made of a polymer having an anion exchange group, the raw material loading compartment and the concentration compartment are divided from each other by a porous membrane made of a polymer having a cation exchange group, and the concentration compartment and the cathode compartment are divided from each other by a microporous membrane. The method of the present invention includes the steps of, in this electrodialysis apparatus, (1) loading a cationic protein-containing aqueous solution into the raw material loading compartment and loading an electrolytic solution into the anode compartment, the concentration compartment, and the cathode compartment, (2) applying a current to the electrodialysis apparatus, and (3) collecting a solution containing a cationic protein from the concentration compartment.