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This paper presents a method for modeling and estimation of the state of charge (SOC) of lithium-ion (Li-Ion) batteries using neural networks (NNs) and the extended Kalman filter (EKF). The NN is trained offline using the data collected from the battery-charging process. This network finds the model needed in the state-space equations of the EKF, where the state variables are the battery terminal voltage at the previous sample and the SOC at the present sample. Furthermore, the covariance matrix for the process noise in the EKF is estimated adaptively. The proposed method is implemented on a Li-Ion battery to estimate online the actual SOC of the battery. Experimental results show a good estimation of the SOC and fast convergence of the EKF state variables.