Novel membranes based on polyphenylene isophthalamide (PA) modified by fullerene derivatives (5 wt% with respect to PA weight) (polyhydroxylated fullerene (fullerenol), carboxyfullerene and fullerene derivative with L-arginine) were developed. The presence of PA/fullerene and PA/fullerene derivative composites and distribution of carbon nanoparticles after ultrasonic treatment in polymer solution was investigated by dynamic light scattering. The influence of carbon modifier on structural characteristics of PA was examined by nuclear magnetic resonance, small-angle X-ray scattering, scanning electron microscopy, atomic force microscopy, sorption experiments, density investigation and contact angle measurements of water. The transport properties were examined by pervaporation separation of industrially important methanol/toluene mixtures in two regimes (1. a series of experiments of different concentrations including azeotropic mixture and 2. only azeotropic mixture) to assess the effect of residual solvent in the PA membranes on their parameters. It was found that all membranes containing fullerene derivatives possessed improved permeation flux compared to pristine PA membrane. The optimal transport characteristics for the separation of methanol/toluene mixtures containing 10–72 wt% methanol were noticed for PA membrane modified by 5 wt% fullerenol due to the highest permeation fluxes (0.084–0.214 kg/(m²h)) and high level of selectivity (95.9 wt% methanol content in the permeate).