A secondary battery system and a method of arranging battery modules capable of recovering and maintaining the system performance are provided. A secondary battery system includes a battery cabinet group including a plurality of battery cabinets each comprising a plurality of battery modules connected to each other, the battery module being a replacement unit, a PCS connected to the battery cabinet group and is controlling charging and discharging thereof, and a battery controller connected to the PCS. The battery controller includes a deterioration inspecting block obtaining a characteristic of the battery modules, a numbering block numbering the battery modules in an ascending order based on the characteristics, and a re-arrangement determining block determining a re-arrangement position of the battery modules in a way that the numbers given by the numbering block are in sequence in the same battery cabinet.