The present work deals with the design of an efficient and inexpensive autonomous photovoltaic array-based water pumping system utilising a new configuration of a single-input balanced dual supply buck–boost DC–DC converter. A four-phase switched reluctance motor (SRM) drive is selected to pump the water effectively and to make the system reliable. The utilised DC–DC converter can provide two balanced outputs using a single solar power source. It offers continuous output supply with minimum ripple to the SRM pump. The new control logic is also discussed in this work to provide equal voltages for two capacitors of the split converter in both starting and steady-state conditions. An improved perturb and observer-based maximum power point tracking control is also utilised to enhance the solar output power at varying irradiance. Moreover, owing to the pulse-width modulation switching of a split converter, a reduction is achieved in the size of split DC-link capacitors. The MATLAB/Simulink-based simulation is done to validate the real-time implementation of a developed system. These obtained responses are again validated through test results obtained via the developed prototype.