Accurate dynamic models of supercapacitors (SCs) are a basis for the design, control and exploitation of the hybrid energy storage systems for electric vehicles. This paper concerns a fractional model of SC impedance, based on the Cole–Cole equation describing relaxation in electric double layer. This article provides a new method of identifying the parameters of fractional order model of SC impedance, performed without disconnecting the SC module from the energy storage system. The test drive for this purpose needs only the respect a few simple recommendations. The article presents the conditions of the mentioned test drive that will ensure the frequency spectra of the recorded signals lying in the bandwidth necessary for the correct identification of the model parameters. These parameters are determined by means of the Nelder–Mead simplex optimization method. The results of the identification described by the time method coincide with those obtained in the frequency domain. It has been shown in the last part of the article that the real energy losses in these systems significantly exceed the losses determined only on the basis of the nominal capacity and series equivalent resistance (ESR), to which the SC catalogue data are usually limited. This paper also provides an auxiliary frequency criterion for the selection of SCs intended for energy storage systems of electric vehicles.