Nafion is a fluorocarbon polymer, commonly used as a proton exchange membrane in fuel cells because of its excellent thermal and mechanical stabilities. However, the basic properties of Nafion, such as its nanostructures and rheological behavior, remain unclear because the morphology of this material is highly sensitive to its processing history. The present work involved a systematic analysis of both the structural and rheological properties of Nafion dispersions carefully prepared using a standard procedure, ranging from dilute (0.1 wt %) to highly concentrated (30 wt %) conditions. Small-angle X-ray scattering confirmed the cylindrical structure of Nafion in dispersion and the unique interactions of Nafion particles acting as polyelectrolytes. Three different scaling relationships involving the zero-shear viscosities of the Nafion dispersions were determined for specific concentration regimes. However, at the upper concentration limit of approximately 30 wt %, the viscosity greatly deviated from these scaling relationships and significant shear thinning was observed. Simultaneous analyses using rheology and small-angle neutron scattering determined fully isotropic spatial correlations on a length scale of less than 60 nm, even when high shear was applied. These results indicate a tightly entangled local structure and the presence of large yet weakly interacting domains that are responsible for the macroscopic shear thinning behavior.