A hydrogen generation system is disclosed that includes a fuel reforming reactor generating a hydrogen-rich reformate gas at a temperature greater than 150 C, a pressure swing adsorption (PSA) hydrogen purification unit that separates the reformate gas into a relatively pure hydrogen stream and an off-gas stream, and a catalytic reactor down stream of the PSA unit that converts carbon monoxide (CO) and hydrogen (H2) contained in the relatively pure hydrogen stream into methane (CH4) and water vapor (H2O). The method of purification involves generating a hydrogen-rich reformate gas at a temperature greater than 150 C in a fuel reforming reactor, separating the reformate gas into a relatively pure hydrogen stream and an off-gas stream in a pressure swing adsorption (PSA) hydrogen purification unit, and converting carbon monoxide (CO) and hydrogen (H2) contained in the relatively pure hydrogen stream into methane (CH4) and water vapor (H2O) in a catalytic reactor down stream of the PSA unit. The hydrogen can be further purified by including a secondary purification stage downstream of the PSA unit and the catalytic reactor wherein the secondary purification stage has a water adsorbent material bed that adsorbs the water vapor H2O and a hydrogen absorbent material downstream of the water absorbent material that absorbs hydrogen gas preferentially, thus concentrating the non-hydrogen components, such as CH4, into an exhaust stream that exits the bed, wherein the absorbed hydrogen gas is then desorbed to create an exiting very pure hydrogen stream.