Disclosed is an apparatus for efficiently managing a battery system in a situation where a charge or discharge power varies with time. The apparatus for managing a battery system includes a power measuring unit configured to measure the magnitude of a charge power supplied to a battery system or a discharge power output from the battery system, a reference setting unit configured to variably set a power distribution reference according to the measured magnitude of power, and a power distributing unit configured to distribute and supply a charge power to battery units having different outputs and capacities according to the set power distribution reference or allow a discharge power to be distributed and output from battery units having different outputs and capacities according to the set power distribution reference.