Lithium-ion batteries are an attractive power source in many scenarios. In some particular cases, including providing backup power for drones, frequency modulation, and powering electric tools, lithium-ion batteries are required to discharge at a high rate (2~20 C). In this work, we present a method to estimate the state of health (SOH) of lithium-ion batteries with a high discharge rate using the battery’s impedance at three characteristic frequencies. Firstly, a battery model is used to fit the impedance spectrum of twelve LiFePO4 batteries. Secondly, a basic estimation model is built to estimate the SOH of the batteries via the parameters of the battery model. The model is trained using the data of six batteries and is tested on another six. The RMS of relative error of the model is lower than 4.2% at 10 C and lower than 2.8% at 15 C, even when the low-frequency feature of the impedance spectrum is ignored. Thirdly, we adapt the basic model so that the SOH estimation can be performed only using the battery’s impedance at three characteristic frequencies without having to measure the entire impedance spectrum. The RMS of relative error of this adapted model at 10 C and 15 C is 3.11% and 4.25%, respectively.