In this paper, an Extended Kalman filter (EKF) based charger for energy storage systems (ESSs) is proposed. Aimed at improved charger availability and galvanic isolation, parallel connected flyback topology is chosen as source interface. Energy storage systems consist of point of load (PoL) converters at their input and hence they behave as instantaneous constant power loads (CPLs). The voltage at the paralleled converters output is the only state variable that is sensed. Using only this information, all other state variables are estimated using EKF. The goal is to overcome the errors while sensing magnetic quantities, reduce the complexity of multi-variable state feedback and to make overall controller design simpler. A flux-estimate based feedback controller is proposed in order to damp the limit cycle oscillations due to CPL. The proposed controller also enables current sharing and provides line and load regulation. Equilibrium points are derived and stability conditions are presented. The validity of the proposed controller is shown using simulation results.