This paper proposes an improved Battery Management System (BMS) that provides active equalization in the battery cells to reduce the total charging time and enhance the system performance. The suggested control scheme can be applied to energy storage systems with Li-ion batteries that are utilized in nearly zero energy building (nZEB) and electric vehicle (EV) microgrids. The proposed BMS is more suitable for the above applications, since repeatable and high dynamic performance from the battery system are required. The improvement in the battery operation and therefore, the enhancement of the whole microgrid performance can be accomplished by properly regulating the charging current of each battery cell through the gate voltage of a parallel connected MOSFET. An Aging Estimator Fuzzy Logic Controller (AEFLC) is also proposed that can online estimates the healthier cell of each battery stack by properly evaluating the internal resistance growth and the capacity fade factor of each cell. Thus, based on the healthier cell, the proposed algorithm controls the MOSFET current in order to achieve the cell equalization. Specifically, an Equalizer Fuzzy Logic Controller (EFLC) evaluates the cells’ voltages and applies the appropriate gate-source voltage (VGS) at each MOSFET. The functionality and the effectiveness of the proposed BMS are verified both for nZEB and EV microgrids via simulation models using the MATLAB/Simulink program. Selective simulation results are presented to validate the operating improvements that the new BMS technique can provide.