Multiport converters (MPCs) that can regulate multiple input/output ports have been proposed to reduce the converter count in electric vehicle battery systems consisting of multiple batteries (12-V, 48-V, and high-voltage batteries). Conventional MPCs consist of an interleaved PWM converter and DAB converter, and an active current balancing control is indispensable for the interleaved converter. Furthermore, the transformer utilization unavoidably decreases because switches are driven with a nominal duty cycle of 0.75 for 48-/12-V batteries. This article proposes a novel MPC with an automatic current balancing capability and improved transformer utilization. A flying capacitor (FC) is added to the interleaved PWM converter to automatically balance inductor currents. The added FC also allows operations with a nominal duty cycle of 0.5 for 48-/12-V batteries, improving the transformer utilization. The experimental verification tests using a 1-kW prototype demonstrated the automatic current balancing capability, improved transformer utilization, and flexible power exchange among three batteries.