Method and system for electrochemically compressing hydrogen. In one embodiment, the system includes a membrane electrode assembly (MEA) that includes a polymer electrolyte membrane (PEM), an anode, and a cathode. First and second gas diffusion media are positioned adjacent the cathode and anode, respectively. A humidifying membrane is positioned next to the second gas diffusion medium on a side opposite the anode. A water supply is connected to the humidifying membrane, and a hydrogen gas supply is connected to the second gas diffusion medium. A hydrogen gas collector including a back pressure regulator is connected to the first gas diffusion medium. Separators, positioned on opposite sides of the MEA, are connected to a power source. In use, hydrogen is electrochemically pumped across the MEA and collected in the hydrogen gas collector. The PEM is kept properly humidified by the humidifying membrane, which releases water into the second gas diffusion medium.