This paper presents a modular circuit structure to generate bipolar high voltage pulses from a low voltage battery source. Smart material based actuators and ion analysers require bipolar high voltage output in the range of ± 1 kV to 3 kV for their effective operation. In this paper, two bidirectional flyback converter modules are connected in differential manner to achieve pulses of opposite polarities respectively. Dedicated CPLD control cards are designed to govern the operation of individual module. Each module operate with a two loop control scheme where inner loop detects Minimum Voltage Point (MVP turn on) and output loop controls the peak charging current. The modules operate in a phase shifted manner with control signals communicated between the individual controllers to ensure module level coordination. An experimental prototype fed from 12 V input is designed and control scheme is implemented to obtain ± 2.5 kV bipolar output voltage. The experimental results observed are in good concordance with the simulation results. © 2018 IEEE.