Novel mixed-matrix electrodialysis heterogeneous ion exchange membranes were fabricated using polyaniline (PANI)-co-graphene oxide (GO) functionalized composite nanoplates. The PANI-co-GO functionalized composite nanoplates were prepared by in situ chemical oxidative polymerization of aniline in the presence of GO nanoplates. The synthesized PANI/GO were characterized by Fourier transform infrared spectroscopy, X-ray diffraction, and scanning electron microscopy. The SEM images demonstrated that utilizing of PANI/GO in membrane matrix led to formation of membranes with a compact structure. Also, more uniform distribution was observed for the incorporated PANI/GO membrane compared to the embedded GO nanoplates ones. The surface hydrophilicity, water content, and ion exchange capacity were enhanced by utilizing PANI/GO composite nanoplates. The membrane potential, transport number, and selectivity were also enhanced in sodium and barium chloride ionic solutions in presence of functionalized nanoplates. The newly prepared membranes showed lower selectivity and transport number for barium ions compared to sodium ions. The sodium and barium flux were enhanced by using PANI/GO. Dialytic rate results showed that modified membranes in this study have good ability in lead ion removal from wastewater. The enhancement in lead flux was more than 50% for the modified membrane containing PANI/GO in comparison with pristine ones.