This book reports on a comprehensive study on the modeling, online and offline parameter estimation and control strategies for fuel cell systems. Upon reviewing the control-oriented modeling of proton-exchange membrane fuel cell systems (PEMFC) and solid oxide fuel cell systems (SOFC), it describes a new a set of methodologies to estimate the parameters of these models, both online and offline. In turn, it reports on the design of different control systems for PEMFC and SOFC. Experimental findings are shown to demonstrate the efficiency of the newly developed methods in practical applications, and their improved performance over classical methods.