In this paper, we propose the algorithm which can control active power and reactive power independently in Battery Energy Storage System. The proposed algorithm is based on the instantaneous power theory that the inner product of the voltage vector and current vector represents the active power and the cross product of those represents the reactive power, and it can control active power and reactive power independently. To verify the validity of the proposed algorithm, we make model of the real power system in th KERI and simulate this algorithm. As a result of this simulation, we verified that the proposed algorithm can control active power and reactive power independently.