This paper presents Type-T thin film thermocouples (TFTCs) fabricated on Kapton (polyimide) substrate for measuring the internal temperature of PBI (polybenzimidazole)-based high temperature proton exchange membrane fuel cell (HT-PEMFC). Magnetron sputtering technique was employed to deposit a 2m thick layer of TFTCs on 75m thick Kapton foil. The Kapton foil was treated with in situ argon plasma etching to improve the adhesion between TFTCs and the Kapton substrate. The TFTCs were covered with a 7m liquid Kapton layer using spin coating technique to protect them from environmental degradation. This Kapton foil with deposited TFTCs was used as sealing inside a PBI (polybenzimidazole)-based single cell test rig, which enabled measurements of in situ temperature variations of the working fuel cell MEA. The performance of the TFTCs was promising with minimal interference to the operation of the fuel cell.