The present invention relates to a method for purifying target protein which contains electron transfer protein, from a protein solution containing the target protein, by means of liquid chromatography. The liquid chromatography is performed as follows: First, the protein solution is introduced into a column which is filled with a packing agent, thereby causing the packing agent to bond to the target protein. Then, impurities are removed, and then the target protein is eluted from the packing agent in an eluent which contains a hydroxy-cholate. An example of the target protein is glucose dehydrogenase which contains a protein having glucose dehydrogenation activity. The liquid chromatography is performed as a combination of hydrophobic chromatography and anion exchange chromatography.