Coarse-grained molecular dynamics simulations, reported in this article, elucidate the self-assembly of semiflexible ionomer molecules into cylindrical bundle-like aggregates. Ionomer chains are composed of hydrophobic backbones, grafted with pendant side chains that are terminated by anionic headgroups. Bundles have a core of backbones surrounded by a surface layer of charged anionic headgroups and a diffuse halo of counterions. Parametric studies of bundle properties unravel the interplay of backbone hydrophobicity, strength of electrostatic interactions between charged moieties, side chain content, and counterion valence: expectedly, the size of bundles increases with backbone hydrophobicity; the aggregate size depends nonmonotonically on the Bjerrum length; increasing the grafting density of pendant side chains results in smaller bundles; and the counterion valence exerts a strong effect on bundle size and counterion localization in the near-bundle region. Results reveal how the ionomer architecture and solvent properties influence the ionomer aggregation and associated electrostatic and mechanical bundle properties. These properties of ionomer aggregates are vital for rationalizing the water sorption behavior and transport phenomena as well as the chemical and mechanical stability of ionomer membranes.