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In spite of various appealing advantages offered by the Proton Exchange Membrane (PEM) fuel cell, including high energy density and near-zero emissions, it is still facing many challenges for commercialization towards reducing cost, improving performance and enhancing durability. Along with optimal performance, the durability of a PEM fuel cell (PEMFC) is greatly improved by the use of a proper control system. A high-quality controller can play a crucial role on the issues concerning fuel starvation and improper water management system. Most of the control schemes reported for PEMFC are either linear or not that effective to adequately address the concerns related to the nonlinear interactive complex system dynamics. Further, the nonlinear control of the integrated PEMFC system that consists of several ancillary units (e.g., air compressor, humidifier, cooling arrangement, and hydrogen and oxygen/air circuit), along with the stack, is rarely studied. This research program aims at the development of a multi input multi output (MIMO) control scheme consisting of the robust state-estimator based extended generic model controller (EGMC) and conventional PI controller for high power PEM fuel cell system operation in space applications.