Designing nanomaterials for drug encapsulation is a crucial, yet challenging, aspect for pharmaceutical development. An important step is synthesizing amphiphiles that form stable supramolecular systems for efficient drug loading. In the case of fluorinated drugs, these have superior properties and also a tendency toward reduced water solubility. For the first time, we report here fluorinated hexosome carriers made from nonionic dendritic amphiphiles, capable of encapsulating the fluorinated drug Leflunomide with high efficiency (62 ± 3%) and increasing its solubility by 12-fold. We synthesized amphiphiles with varying tail groups (fluorinated/alkylated), and their supramolecular self-assembly was investigated using cryogenic transmission electron microscopy and small-angle X-ray scattering. Furthermore, Leflunomide and its equivalent nonfluorinated counterpart were encapsulated within fluorinated and nonfluorinated assemblies. Self-assembly and encapsulation mechanisms were well supported by coarse-grained molecular simulations, yielding a fundamental understanding of the new systems.