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This article presents a novel microprocessor-based controller for high-temperature proton-exchange membrane (HTPEM) fuel cells. The controller manages start-up, control, protection, shut-down, and monitoring functions. This portable unit controls HTPEM fuel cell components to ensure secure and reliable operation in both normal and transient operation modes. The proposed controller monitors critical fuel cell parameters such as cell voltages, air/hydrogen inlet temperatures, air/hydrogen inlet pressures, stack temperature, and stack current. The controller software has several concurrent control loop tasks, which send proper commands to the fuel cell system. The hardware consists of a development microchip board and a novel interface input-output (I/O) board, including a liquid crystal display (LCD) and a keyboard.