A voltammetric method is developed for the determination of quercetin and rutin in the simultaneous presence on a glassy carbon electrode modified with carbon nanofibers and polythymolphthalein. The conditions of the potentiodynamic electrolysis of thymolphthalein providing the maximum difference in the oxidation potentials of quercetin and rutin equal to 136 mV are found. Thymolphthalein electropolymerization should be carried out in a 100 μM solution by the 10-fold cycling of the potential from 0 to 1.7 V at a sweep rate of 75 mV/s in phosphate buffer solution with pH 7.0. The electrode modified with polythymolphthalein is characterized by scanning electron microscopy, cyclic voltammetry, and electrochemical impedance. It is found that the oxidation of quercetin proceeds irreversibly, and that of rutin, quasi-reversibly with the participation of two electrons and two protons and is controlled by the adsorption of analytes on the electrode surface. The analytical range is 0.025–1.00 μM for both analytes, and the limits of detection are 7.3 nM for quercetin and 4.7 nM for rutin. The selectivity of the electrode response to quercetin and rutin in the presence of inorganic ions, saccharides, and ascorbic and p-coumaric acids is shown. The developed method is tested on real samples (linden Tilia L. flowers and onions).