The objective of this paper is to investigate the effects of hydrogen supply schemes on the efficiency of a proton exchange membrane (PEM) fuel cell system. Three different hydrogen supply schemes are examined: the flow-through mode, the dead-end mode, and the recirculation mode. The electrochemical performance of the flow-through mode, determined using a commercial test station, is used to provide a benchmark for the design of the fuel cell generators operated in either the dead-end or recirculation modes. Smart control algorithms for the dead-end and recirculation hydrogen delivery modes are proposed to minimize waste from the supplied hydrogen and to avoid performance degradation due to excess water and nitrogen accumulation in the anode channels. The transient variations in flow and electrochemical characteristics of the dead-end and recirculation modes are measured and discussed in detail. Finally, a comparison of the stack and system efficiencies of the dead-end and recirculation modes is performed.