Ultrasonic bonding, with its extremely fast cycle times and energy efficiency, is being investigated as an important manufacturing technology for future mass production of fuel cells. The objectives of the authors’ research are to (1) create a multi-physics simulation model that predicts through-thickness energy distribution and temperature gradients during ultrasonic sealing of polybenzimidazole (PBI) based Membrane Electrode Assemblies (MEAs) for High Temperature PEM fuel cells, and (2) correlate the model with experimentally measured internal interface (e.g., membrane/catalyst layer) temperatures. The multi-physics model incorporates the electrode and membrane material properties (stiffness and damping) in conjunction with the ultrasonic process parameters including pressure, energy flux and vibration amplitude. Overall, the processing of MEAs with ultrasonic bonding rather than a hydraulic thermal press results in MEAs that meet or exceed required performance specifications, and potentially reduces the manufacturing time from minutes to seconds.