A method for operating a water electrolysis system includes determining whether or not a water electrolysis apparatus is shut down. The water electrolysis system includes the water electrolysis apparatus, a water circulation apparatus, and a gas-liquid separation apparatus. The water electrolysis apparatus includes power feeders provided on an anode side and a cathode side of an electrolyte membrane. The water electrolysis apparatus generates oxygen on the anode side and generates hydrogen on the cathode side at a higher pressure than a pressure of the oxygen by electrolysis of water. Pressure on the cathode side is released when it is determined that the water electrolysis apparatus is shut down. The water circulation apparatus is operated until a concentration of hydrogen remaining on the anode side is a specified value or less under a condition in which a release of pressure on the cathode side is completed.