Electrochemical impedance measurements of lithium ion batteries (LIBs) in energy storage systems (ESS) were performed. Square-current electrochemical impedance spectroscopy (SC-EIS), which is a simple and cost-effective approach to measure impedance, was chosen to investigate a large-scale LIB system. Harmonics calculated by Fourier transform from a square waveform were used to determine the impedance. On the basis of a simple electrochemical reaction involving the ferri/ferro-cyanide redox couple and the LIB, the accuracy of the impedance measurement was found to depend on both the signal-to-noise ratio of the power spectra of the harmonics as well as the attenuation rate of the “measured value of impedance” and the “theoretical spectra value” from Fourier series. The accuracy was improved by adjusting the input waveform to be close to an ideal square waveform from Fourier series. The accuracy was further improved by the combined use of a simple moving average and an overall average. The impedance from a degraded square waveform generated by a cost-effective power controller was able to be determined by increasing the measurement time, which aided averaging. By designing the input signal to be close to an ideal square waveform from Fourier series, kilowatt-class LIB modules/cubicles in an ESS was able to be measured. Moreover, a degraded LIB module in an ESS was able to be detected using EIS, which highlights the utility of this technique for in situ impedance measurements of large-scale LIB systems.