An electrochemical model based capacity fade estimation method for a Li-Ion battery is investigated in this paper. An empirical capacity fade model for estimating the state of health of a LiFePO4 electric vehicle battery was integrated with electrochemical battery model in Matlab/Simulink platform. This combined model was then validated against experimental data reported in the literature for constant current charge / discharge cycling. An HPPC current profile was then applied to the validated electrochemical-empirical battery prognosis model which reflected a real-time operating condition for charge and discharge current fluctuations in an electric vehicle battery. The combined model was simulated under the two different HPPC current inputs for three different cycle times. Additionally temperature was taken in account in estimating the cycle aging under the applied current profile to assess the present capacity remaining in the battery. The simulation results provided the state of health (SOH) of the battery for these cycling times which were comparable to the published experimental SOH values for constant current charge/discharge profiles. Thus this model can potentially be used to predict the capacity fade status of an electric vehicle battery.