High-temperature proton exchange membrane fuel cells (HT-PEMFC) directly convert hydrogen and oxygen to produce electric power at a temperature significantly higher than conventional low-temperature fuel cells. This achievement is due to the use of a phosphoric acid-doped polybenzimidazole membrane that can safely operate up to 200 °C. PBI-based HT-PEMFCs suffer severe performance limitations, despite the expectation that a higher operating temperature should positively impact both fuel cell efficiency and power density, e.g., improved ORR electrocatalyst activity or absence of liquid water flooding. These limitations must be overcome to comply with the requirements in mobility and stationary applications. In this work a systematic analysis of an HT-PEMFC is performed by means of electrochemical impedance spectroscopy (EIS), aiming to individuate the contributions of components, isolate physical phenomena, and understand the role of the operating conditions. The EIS analysis indicates that increases in both the charge transfer and mass transport impedances in the spectrum are negatively impacted by air humidification and consistently introduce a loss in performance. These findings suggest that water vapor reduces phosphoric acid density, which in turn leads to liquid flooding of the catalyst layers and increases the poisoning of the electrocatalyst by phosphoric acid anions, thus hindering performance.