Recent neuroscience studies have suggested that controlling the excitation and inhibition (E/I) balance is essential for maintaining normal brain function. However, while control of time-varying E/I balance is considered essential for perceptual and motor learning, an efficient method for estimating E/I balance changes has yet to be established. To tackle this issue, we propose a method to estimate E/I balance changes by applying neural-mass model-based tracking of the brain state using the Ensemble Kalman Filter. In this method, the parameters of synaptic E/I gains in the model are estimated from observed electroencephalography signals. Moreover, the index of E/I balance was defined by calculating the ratio between synaptic E/I gains based on estimated parameters. The method was validated by showing that it could estimate E/I balance changes from human electroencephalography data at the sub-second scale, indicating that it has the potential to quantify how time-varying changes in E/I balance influence changes in perceptual and motor learning. Furthermore, this method could be used to develop an E/I balance-based neurofeedback training method for clinical use.