Proton exchange membrane fuel cells (PEMFCs) are a promising clean energy technology; however, effective thermal management remains a critical challenge, particularly at high power densities, where temperature imbalances can severely impact stack performance and longevity. Boiling cooling, which utilizes the phase change of the coolant, presents a potential solution to enhance thermal management in PEMFCs. Despite its promise, its practical application in fuel cell stacks has not been fully explored. This study aims to address this gap by developing a performance testing platform to assess the temperature characteristics and output performance of PEMFCs under boiling cooling conditions. Temperature uniformity was evaluated using the wall temperature difference (Td) and the temperature uniformity index (TUI), with a focus on the effects of coolant inlet temperature and mass flux. A univariate experimental design was employed to systematically investigate the impact of five critical operational parameters—coolant inlet temperature, mass flux, hydrogen flow rate, humidifier temperature, and exhaust back pressure—on PEMFC performance. The results demonstrate that boiling cooling significantly improves temperature uniformity, with TUI improvements of approximately 47.69 % for Cell 1 and 58.58 % for Cell 3, especially at high current densities. In comparison to single-phase cooling, boiling cooling exhibited superior thermal management capacity, maintaining stable output at higher power densities. Furthermore, the stack’s power output was improved by 9.04 % under boiling cooling. The optimization of operational parameters, such as hydrogen flow rate, humidifier temperature, and exhaust back pressure, was shown to enhance reaction efficiency and mitigate issues such as membrane dehydration and flooding. These findings validate the effectiveness of boiling cooling as a robust thermal management solution for PEMFCs, highlighting the importance of parameter optimization for further improving fuel cell performance and reliability.