Zero-emission transportation is currently a public priority, especially in big cities. For this reason, the use of electric vehicles (EVs) is receiving much attention. To facilitate the adoption of EVs, a proper charging infrastructure together with energy management is essential. This article proposes a design guideline for a direct current (DC) charging station with bipolar properties. A bipolar system can convert a two-wire system into three wires in a microgrid system with a neutral line. The configuration of the bipolar system supports different loads; therefore, the unbalanced operation is inherent to the system. The proposed bipolar DC charging station (CS) has a three-level balancing converter that reduces the step-down effort chargers. Moreover, this paper proposes the continuous-control-set model predictive control (CCS-MPC)-based balancing strategy that allows the handling of different output loads while keeping the neutral-line voltage efficiently regulated with improved dynamic performance compared to a traditional controller. Stability and parameter robustness analyses are also performed for the control parameter selection. To ensure the performance of the proposed method, both simulation and experimental results are presented and compared with those obtained from the traditional methods.