Although an increasing number of researchers are developing electroanalytical protocols for the chiral recognition of amino acids, the electroactive units of the tested isomers still need to provide corresponding electrical signals. In this study, a supramolecular system was developed for the chiral electroanalysis of amino acids regardless of electroactive units. As a model system, an enantiopure electroactive molecule Fc-(S,S)-1 that includes a ferrocenyl group was synthesized and acted as a guest. Moreover, hydrophobic cyclobis-(paraquat-p-phenylene) (CBPQT4+-2) was used as the host. In the presence of π-π stacking and the attraction of π-electrons, CBPQT4+-2 can encapsulate Fc-(S,S)-1 into its cavity. Next, a screen-printed electrode was utilized for electrochemical chiral recognition. The host was fixed on the surface of the working electrode, and the guest was used as the electroactive chiral selector to support electron transfer. Once different configurations of amino acids (threonine, histidine, glutamine, and leucine) were mixed with the guest, regardless of whether they contained electroactive units, differences in the cyclic voltammetry results of the probe enantiomers could be observed, namely, in the peak currents or peak potentials. However, glutamine was an exception because the L-isomer had a stronger binding affinity with Fc-(S,S)-1 + Cu(II), which would limit the transport of the complex into the cavity of CBPQT4+-2, thereby resulting in a low peak current. Thus, an inverse phenomenon was observed with glutamine. In summary, we believe that this work can increase the testing scope for the chiral recognition of different kinds of isomers using electrochemical tools.