Carbon monoxide (CO), which is preferentially absorbed on the platinum catalyst layer of a proton exchange membrane fuel cell (PEMFC), is extremely detrimental to cell performance. Essentially, the carbon monoxide absorption diminishes the cell’s performance by blocking and reducing the number of catalyst sites available for the hydrogen oxidation reaction. In order to obtain a full understanding of CO poisoning characteristics and remediate CO-poisoned PEMFCs, a CO poisoning numerical model is developed and incorporated into a fully three-dimensional electrochemical and transport coupled PEMFC model. By performing CFD numerical simulations, this paper clearly demonstrates the CO poisoning mechanisms and characteristics of PEMFCs. The predictive capability for CO poisoning effects enables us to find major contributors to CO tolerance in a PEMFC and thus successfully integrate CO-resistant fuel cell systems.