A portable proton exchange membrane (PEM) fuel cell–battery power system that uses hydrogen as fuel has a higher power density than conventional batteries, and it is one of the most promising environmentally friendly small-scale alternative energy sources. A general methodology of modeling, control and building of a proton exchange membrane fuel cell–battery system is introduced in this study. A set of fuel cell–battery power system models have been developed and implemented in the Simulink environment. This model is able to address the dynamic behaviors of a PEM fuel cell stack, a boost DC/DC converter and a lithium-ion battery. To control the power system and thus achieve proper performance, a set of system controllers, including a PEM fuel cell reactant supply controller and a power management controller, were developed based on the system model. A physical 100W PEM fuel cell–battery power system with an embedded micro controller was built to validate the simulation results and to demonstrate this new environmentally friendly power source. Experimental results demonstrated that the 100W PEM fuel cell–battery power system operated automatically with the varying load conditions as a stable power supply. The experimental results followed the basic trend of the simulation results.