A protein-inspired ion-imprinted polymer (IIP) was used as an additive in a carbon paste electrode for the selective determination of copper(II) in water samples. The imprinted polymer was synthesized by precipitation polymerization of a functional monomer, methacrylamido-L-histidine (MAH), based on an amino acid, L-histidine, with ethylene glycol dimethacrylate (EGDMA) as crosslinker. The corresponding non-imprinted polymer (NIP) and a copolymer containing EGDMA and methyl methacrylate (MMA) (in the same proportions as MAH in the NIP) were also prepared in similar conditions as the IIP. The polymer particles were first chemically characterized by 13C CP-MAS NMR and FT-IR and the presence of MAH was confirmed by the colorimetric Pauly's test. It was shown by SEM and adsorption/desorption of nitrogen that the IIP and the NIP present similar morphological properties. The copper(II) binding properties of the polymers were also studied in a batch adsorption experiment, and an imprinting effect was observed for the IIP. This polymer was shown to possess binding cavities selective towards copper(II) versus common interferents (iron(III), zinc(II) and lead(II)), when compared to the NIP and to the poly(EGDMA-co-MMA). A carbon paste working electrode was prepared with the IIP particles and a limit of detection of 59 nmol/L for copper(II) was determined in a potassium phosphate buffer (0.1 M, pH = 7). The determination of copper(II) was not affected by the presence of a 50-fold excess of iron(III), zinc(II) and lead(II). Finally, the copper concentration in a real seawater was estimated to be 0.12 μmol/L, in full agreement with a measurement by polarography which was used as a reference method.