This paper proposes a design method for a secondary battery system using an active-neutral point clamped (A-NPC) inverter. The proposed system consists of a secondary battery, 3-level DC/DC converter, DC-link capacitor, and bi-directional A-NPC inverter, respectively. The conventional neutral point clamped (NPC) inverter has limitation on switching the switching loss of IGBT into a particular element to increase the switching frequency. This paper proposes a modulation method for implementing the A-NPC converter instead of the existing NPC converter to address the loss of the unbalances. The simulation verifies the validity of the analysis results and the validity of the secondary cell charging system by suggesting the analysis results of the IGBT according to the modulation method.