This article experimentally investigated how to optimize system performance of a proton exchange membrane fuel cell (PEMFC) stack system via various operation and control processes. The main goal of this study was to allow this PEMFC system to meet practical variable loads while maintaining the rating capacity of the PEMFC stack. The current study used a PEMFC stack with a rating capacity of 2.5 kW. A fully automated fuel cell test bench was used to perform the optimization study. The test bench consisted of a 2.5 kW fuel cell stack, hydrogen supply subsystem, air supply subsystem, water and heat management subsystem, power conditioning subsystem and system control and data acquisition subsystem. The 2.5 kW PEMFC was tested on the test bench to find the optimum control strategy. Long term tests of the current study showed that by appropriate manipulation of the control strategies, power output of this PEMFC system could reach rated or designed capacity.