A physics-based theoretical model that predicts the chemical degradation of the perfluorosulfonic acid polymer electrolyte membrane during fuel cell operation is developed. The model includes the transport and reaction of crossover gases, hydrogen and oxygen, to produce radicals in the membrane that subsequently react with the polymer to release hydrogen fluoride. The model assumes that a uniform distribution of nanometer-sized platinum deposits in the membrane (as a model input) originating from cathode dissolution provides the sites for radical generation. The degradation rate, measured by the release of hydrogen fluoride, depends on the net radical generation sites in the membrane, the concentration of the crossover gases, the hydration level of the membrane, the operating temperature, the operating voltage, and the thickness of the membrane. The model-predicted trends agree well with those reported and with our experimental results reported in the first article of this series by Madden et al. [J. Electrochem. Soc., 156, B657 (2009)]. Furthermore, the model provides insight to the factors that affect radical generation vs radical quenching, which aids in explaining the experimentally observed nonlinear trends of fluoride emission with reactant concentration and membrane thickness. (C) 2010 The Electrochemical Society. [DOI: 10.1149/1.3481450] All rights reserved.