The invention provides a system and a method for generating high pressure hydrogen that is able to efficiently and safely generate hydrogen by only the electrolysis of water even when using electric power generated by a frequently varying natural energy, such as sunlight, without using any compressors. The system comprises an electrolysis cell using polyelectrolyte membranes, particularly a double-polarity multi-layered type electrolysis cell having a specified structure disposed in a vessel for storing generated hydrogen, preferably for storing cooled hydrogen under a high pressure hydrogen atmosphere. High pressure hydrogen is generated by electrolysis of pure water using the electrolysis cell by suppressing the pressure applied to the cell to a pressure below the pressure resistance of the cell using a differential pressure sensor and pressure controller.