Ion-containing block copolymers hold promise as next-generation proton exchange membranes in hydrogen and methanol fuel cells. These materials' self-assembled ordered nanostructures facilitate proton transport over a wide range of conditions, a requirement for robust fuel cell performance. In this perspective, we will present an overview of the morphology and transport properties of ion-containing block copolymers that have been studied to gain insight into the fundamental behavior of these materials and, in some cases, are targeted toward applications in fuel cells and other electrochemical devices. We will discuss the challenges associated with predicting and obtaining well-ordered morphologies in block copolymers with high ion content, particularly those with chemistries that can withstand the chemical and mechanical stresses of the fuel cell, such as aromatic backbone block copolymers. New opportunities for ion-containing block copolymers in alkaline membrane fuel cells will also be reviewed.