This study demonstrates a facile yet effective strategy for amperometric assay of electrochemically inactive heparin based on an anion-exchange mechanism with polyimidazolium (Pim) as the synthetic receptor. The rationale for the amperometric heparin assay is essentially based on the different binding affinity of the synthetic Pim receptor toward electrochemically active ferricyanide (Fe(CN)6(3-)) and electrochemically inactive heparin. To accomplish the amperometric assay, Pim is first synthesized and used as the artificial receptor to recognize the anions (i.e., Fe(CN)6(3-) and heparin). The stronger binding affinity of the synthetic Pim receptor toward heparin than toward Fe(CN)6(3-) essentially validates the amperometric heparin assay through an anion-exchange mechanism with the decrease in the redox peak current of Fe(CN)6(3-) adsorbed onto the Pim film as the signal readout. The anion exchange between Fe(CN)6(3-) and heparin on the Pim receptor is verified by cyclic voltammetry and Fourier transform IR and UV-visible spectroscopies. The ratio of the current decrease shows a linear relationship with heparin concentration with a concentration range from 0.5 to 10 μM. With animal experiments by dosing intraperitoneally and collecting the serum sample, the method is demonstrated to be potentially useful for investigating heparin metabolism in the biological system. This study not only provides a simple yet effective route to a heparin assay but also opens a new way to developing amperometric methods for electrochemically inert species by fully utilizing the supramolecular principles.