Accurately estimating the state of charge (SoC) in battery management systems (BMSs) requires the measurement of numerous parameters and advanced algorithms. This work studies multifrequency ultrasonic waves to estimate the SoC of Li-ion batteries by sensing the material changes during charge/discharge. A pouch-type LiNi0.6Mn0.2Co0.2O (NMC622)graphite battery cell is designed and fabricated with a capacity of 2.4 Ah. Different ultrasonic testing setups are explored to determine the optimal testing parameters for the battery. An ultrasonic monitoring system is developed to monitor the battery during charge/discharge at 750 kHz, 1 MHz, and 1.5 MHz. Signal processing algorithms are proposed for extracting three ultrasonic features—amplitude, wave velocity, and attenuation. In a three-cycle test, the amplitude histories do not show clear correlations with the SoC. The wave velocities of all three frequencies have an approximately linear relationship with the SoC, which can be used for SoC estimation. Hysteresis behavior is observed for the wave velocity in terms of a larger slope in the discharge process and velocity drop after a close charge/discharge cycle. The wave attenuation is able to capture the material phase transitions during charge/discharge.