The packed bed thermal energy storage (PBTES) system is a versatile solution for storing solar thermal energy and waste heat at various temperature levels. Enhancing the heat transfer coefficient between the encapsulation material and the heat transfer fluid (HTF) is crucial for improving the system’s thermal performance. This study used stainless steel spherical balls to encapsulate myristic acid as the phase change material (PCM) and water as the HTF. Experimental investigations were conducted on a lab-scale rectangular storage tank, examining three different HTF flow rates (200 LPH, 300 LPH, and 400 LPH) during the charging and discharging phases. The results demonstrated that increasing the flow rate reduced the charging/discharging durations of the PCM, enabling efficient heat energy storage/release within a shorter time. Notably, the cumulative heat stored/released was higher than other HTF flow rates at the 80-minute charging phase and the 105-minute discharging phase for the flow rate of 400 LPH. The PBTES system demonstrated an average energy efficiency of 85.79% and an exergy efficiency of 34.29%. The thermo-hydraulic assessment of this study confirmed that higher HTF flow rates significantly improved the overall performance of the PBTES system.