A simple proportional integral (PI) controller with scheduled gain has been developed and implemented in a catalytic membrane reactor (CMR) to obtain pure hydrogen from a methanol steam reforming process. The controller is designed to track the setpoint of the pure hydrogen flow rate in the permeate side of the CMR via the manipulation of the fuel inlet flow rate. Therefore, the controller actuator is the liquid pump that provides the mixture of methanol and water to the reactor. Within the CMR, the catalytic pellets of PdZn/ZnAl2O4/Al2O3 have been used to facilitate the methanol steam-reforming reaction under stoichiometric conditions (S/C = 1), and Pd–Ag metallic membranes have been employed to simultaneously separate the generated hydrogen. The PI controller design is based on a mathematical model constructed using transfer functions acquired from dynamic experiments conducted with the CMR. The controller has been successfully implemented, and experimental validation tests have been carried out at 450 °C and relative pressures of 6, 8, 10, and 12 bar.