The aim of this study is to prepare Cr(VI) ion-imprinted polymer (IIP) grafted on the surface of functionalized polyacrylonitrile nanofibrous mat (FPANFM), IIP-functionalized-PANFM, for the removal of Cr(VI) from aqueous solutions. The prepared materials were characterized by FT-IR, TGA, FESEM, and energy dispersive X-ray spectroscopy (EDS). Moreover, various operating conditions such as contact time, initial metal ion concentration (5–500 mg L−1), IIP-functionalized-PANFM dosage and FPANFM/IIP weight ratio. The imprinting efficiency was evaluated by comparing the adsorbed amount of Cr(VI) by IIP and IIP-functionalized-PANFM with the adsorption by the non-imprinted polymer (NIP). Cr(III), Cu(II), and Cd(II) were selected as interferences and used individually to study the selectivity factor. The maximum adsorption capacity was<30 mg g−1 for NIP, PANFM, and FPANFM, while for IIP and IIP-functionalized-PANFM was 183 mg g−1 and 398 mg g−1 in a very short time (12 min.), respectively. Moreover, the reusability of the IIP and IIP-functionalized-PANFM was tested for several times and no significant loss in adsorption capacity was observed. Also, isotherm models, kinetic adsorption mechanism and thermodynamic parameters were investigated.