The integration of solar-powered pumping systems (SPPS) into agriculture and potable and wastewater sectors becomes mandatory to provide water in remote regions. The broad use of SPPS with classical maximum power point tracking controllers (MPPTCs) showed moderated voltage and power response deterioration. Therefore, the necessity for overcoming these performance degradations and pre-testing of MPPTCs is not an option for the proper operation of such systems. This paper presents a new simple, cost-effective real-time hardware-in-the-loop (RT-HIL) framework to enhance the dynamic performance of SPPS. To accomplish this study, a real pumping station was modeled and equipped with MPPTCs through matlab/simulink. Besides, a practical SPPS was implemented to evaluate the effectiveness of the proposed RT-HIL on system performance. The practical SPPS includes designing a DC-DC buck converter circuit equipped with metaheuristic optimization-based real-time MPPTCs. The tuned PI/FOPI-based MPPTCs are adopted in this work to gain the maximum power from the PV generator under measured real environmental conditions. The proposed real-time MPPTCs techniques are perturb and observe, and incremental conductance (IC) with I, PI, and fractional-order PI (FOPI) controllers. The simulation and the experimental results prove the superiority of the developed real-time FOPI-based MPPTCs in enhancing the system performance in terms of the gained power, module output current, pump flowrate, and pump efficiency. The paper’s novelty lies behind the relatively low-cost real-time execution of PI/FOPI-based MPPT techniques on SPPS. This work was simulated using matlab/simulink in conjunction with Arduino-based RT-HIL and the experimental validation was implemented at the National Water Research Center (NWRC) in Egypt.