A sensitive and selective electrochemical sensor based on ion-imprinted chitosan-graphene nanocomposites (IIP-S) has been developed for the determination of Cr(VI). The ion-imprinted polymers were constructed by one-step electrodeposition. The morphology and structure of IIP-S were characterized by SEM, TEM, XRD, FTIR and EDS, respectively. Meanwhile, the electrochemical behavior of IIP-S was investigated using CV, EIS and DPV. The linear range of IIP-S was from 1.0 × 10 to 1.0 × 10 mol/L, with the low detection limit of 6.4 × 10 mol/L (S/N = 3). The sensor exhibited high selectivity for the determination of Cr(VI) in the presence of Zn(II), Co(II), Cu(II), Ni(II), Mn(II), MnO, CO, SO and MoO ions. The IIP-S also provided excellent stability and good repeatability that the sensitivity remained 85% after 9 cycles of rebinding-removal, while the sensitivity retained 87% of its initial response storing at 4 °C for 17 days. Moreover, it was successfully applied to the detection of Cr(VI) ions in tap water and river water.