The miniaturization and increasing functionality of electronic devices lead to significant heat generation, negatively impacting their performance and longevity. Efficient thermal management is crucial to maintain temperature within safe operating limits. Using nanofluids in mini-channel heat sinks and optically tuned nanofluids in agricultural greenhouses has emerged as a viable solution for active cooling. This study investigates the thermal cycling performance of PCM-based heat sinks with and without pin fins to assess their suitability for long-term thermal management applications. Thermal cycling tests are conducted on PCM-based heat sinks containing RT-42 PCM and different pin fin configurations made from aluminum 2024-T851. The tests evaluated stability under a constant 10 W heat flux during both charging and discharging phases for baseline cases without fins. The results indicate that the maximum temperature difference between the 30th and 40th thermal cycles was only 0.97 °C, representing a mere 2.08% variation. This observation highlights the ability of PCM-based heat sinks to maintain a consistent temperature profile even under repeated thermal loading conditions. The PCM-based triangular pin fin heat sink was more effective than the circular and square pin fin heat sinks. It maintained the lowest average temperature at 32.83 °C and had the lowest rate of temperature increase during charging, at 0.463 °C per minute. Furthermore, the combination of PCM and triangular fins demonstrated superior thermal stability compared to other configurations. The maximum temperature difference between the first and 40th thermal cycles for this configuration is observed at only 0.83 °C with 1.38% variation. This exceptionally low-temperature difference underscores the effectiveness of the triangular pin fin design in promoting heat dissipation and maintaining thermal stability. The results highlight the potential of PCMs to enhance the long-term performance of electronic devices by maintaining optimal operating temperatures.