An original approach for rapid voltammetric determination of the hemagglutinin (HA) protein using original new triazoloazine-based compounds as agents of biomolecule recognition was developed. A pronounced redox activity of original molecules was established; a possible mechanism of electrochemical conversion was proposed. The peak current of the nitro group electroreduction was chosen as an analytical signal. An efficient method for immobilizing the molecules on the surface of carbon nanotubes using thiol-ene and thiol-ine reactions with the radical initiator azobisisobutyronitrile has been proposed. The binding constants of the “compound-hemagglutinin” interaction were determined experimentally without and with external potential and calculated by the molecular modeling method. Compound 2-methylthio-6-nitro-7-oxo-4-propylene-1,2,4-triazolo-4,7-dihydro[5,1-c]-1,2,4-triazine(1a) showed the best characteristics of selective binding to the biotarget. A dependence of the analytical signal on the concentration of hemagglutinin in probe I* = -(13.1 ± 0.5) lgC + (93±2) was obtained in the range 10−7–10−3 M, the limit of detection calculated by the 3-sigma criteria was 7.0 10−8 M. The proposed approach has been successfully tested on saliva model solutions and anti-influenza vaccines.