As the focus on proton exchange fuel cells continues to escalate in the era of alternative energy systems, the rational design of sulfonated polymers has emerged as a key technique for enhancing device efficiency. Although the synthesis and characterization of a wide variety of sulfonated polymers have been extensively reported over the last decade, quantitative understanding of the factors governing the ion transport properties of these materials is in its infancy. In this article, we describe the current understanding of the thermodynamics and ion transport in sulfonated polymers. Various strategies for accessing improved transport properties of sulfonated polymers are presented by focusing on their structure-property relationship. The major accomplishment of obtaining well-defined morphologies for these sulfonated polymers is highlighted as a novel means of controlling the transport properties. Recent studies on the thermodynamics, morphologies, and anhydrous transport properties of sulfonated block copolymers comprising ionic liquids, geared towards high temperature polymer electrolyte membranes as a prospective technology, are also expounded.