In a method of stopping an operation of a water electrolysis system, an on-off valve disposed in a pressure release line communicating with a cathode side of an electrolytic membrane is opened while an electrolytic current is applied between power feeders to electrolyze water for generating oxygen on an anode side of the electrolytic membrane and high pressure hydrogen having a higher pressure than a pressure of the oxygen on the cathode side. A value of the electrolytic current is reduced in a predetermined cycle or continuously. One of a specific resistance and conductivity of water to be supplied to the high pressure hydrogen producing apparatus is detected. The value of the electrolytic current is increased if the specific resistance is equal to or lower than a first predetermined value, or if the conductivity is equal to or higher than a second predetermined value.