State-of-charge (SOC) is one of the significant indicators to estimate the driving range of the electric vehicle and to control the alternator of the conventional engine vehicles as well. Therefore its precise estimation is crucial not only for utilizing the energy effectively but also preventing critical situations happening to the power train and lengthening the lifetime of the battery. However, lead-acid battery is time-variant, highly nonlinear, and the hysteresis phenomenon causes large errors in estimation SOC of the battery especially under the frequent discharge/charge. This paper proposes a novel estimation technique for the SOC of the Lead-Acid battery by using a well-known Extended Kalman Filter (EKF) and an electrical equivalent circuit model of the Lead-Acid battery considering diffusion and hysteresis characteristics. The diffusion is considered by the reconstruction of the open circuit voltage decay depending on the rest time and the hysteresis effect is modeled by calculating the normalized integration of the charge throughput during the partial cycle. The validity of the proposed algorithm is verified through the experiments.