This paper presents operation and control systems for a new modular on-board charger (OBC) based on a SEPIC converter (MSOBC) for electric vehicle (EV) applications. The MSOBC aims to modularise the battery units in the energy storage system of the EV to provide better safety and improved operation. This is mainly achieved by reducing the voltage of the battery packs without sacrificing the performance required by the HV system. The proposed MSOBC is an integrated OBC which can operate the EV during traction and braking, as well as charge the battery units. The MSOBC is composed of several submodules consisting of a full-bridge voltage source converter connected on the ac side and SEPIC converter installed on the battery side. The SEPIC converter controls the battery segments with a continuous current because it has an input inductor which can smooth the battery’s currents without the need for large electrolytic capacitors. The isolated version of the SEPIC converter is employed to enhance the system’s safety by providing galvanic isolation between the batteries and the ac output side. This paper presents the necessary control loops to ensure the optimal operation of the EV with the MSOBC in terms of charge and temperature balance without disturbing the required modes of operation. The mathematical analyses in this paper are validated using a full-scale EV controlled by TMS320F28335 DSP.