Battery energy storage systems are widely used in microgrid for mitigating the power fluctuations caused by the intermittent nature of the renewable energy sources (RES). This paper considers the vanadium redox flow battery (VRB) based energy storage system as it has very long cycle life, deep discharge capability, high energy efficiency and no cell-balancing issues. In case of the islanded microgrid, the charging process of VRB based energy storage system is vastly affected by variable power from RES. The conventional charging schemes may fail to charge, be affected by greater current tracking error and may create gassing side reactions (oxygen and hydrogen evolutions) which significantly degrades the health and the performance of VRB. To alleviate these limitations, this paper presents an advanced charging control scheme for VRB based energy storage system to deal with the variable input power. The proposed control approach is based on the first principle model of VRB which calculates the charging current based on the available power from RES. Moreover, the proposed control scheme accurately determines the limiting current based on the charging current and surface concentration boundary of the vanadium ions and electrolyte flow rate. This limiting current determination is the key contribution of this paper which works as a control constraint and protects the VRB from overcharging and gassing side reactions. The proposed charging scheme is applied through a PI-controller based single phase shifted (SPS) isolated dual-active-bridze (DAB) dc-dc converter.