The ability of piperazine-based ionic liquids, comprising eco-friendly anions, for fuel dearomatization is analyzed using molecular dynamics simulation techniques. Pure ionic liquids and their methanol mixtures were studied as extracting agents. The properties of aromatic extraction from a model fuel, composed of n-heptane + toluene, were studied from a nanoscopic viewpoint. The structural and energetic properties of the studied extracting agents and the behavior of aromatics on the ionic liquid phases were analyzed and related to the aromatic extraction ability. Dynamic aspects of the extraction process, such as the diffusion rates and interfacial behavior, were also analyzed. The reported results provide relevant information on the aromatic extraction mechanism from fuels using ionic-liquid-based extracting agents, showing a platform for developing useful extraction fluids based on environmentally friendly fluids, which may be competitive with extraction processes based on traditional fluids.