Misalignment in the flow field plates of High-Temperature Polymer Electrolyte Membrane Fuel Cell (HT-PEMFC) due to manufacturing tolerances, assembly process, or unavoidable vibration during the cell operation is contemplated its performance and durability. This study investigates the effect of flow field plate misalignment and its concomitant impact with varying the clamping pressures on HT-PEMFC operation. The study considers six degrees of cathode flow field misalignment, varying from 0% to 100% with respect to the anode flow field. Clamping pressures ranging from 1 to 2 MPa are applied to the various cases of misalignment to study their effect on GDL deformation and intrusion into the channels. The structural analysis shows that as the misalignment increases from 0 to 100%, the GDL compression increases from 26.72% to 37.75% for 1 MPa, 40.07% to 56.63% for 1.5 MPa, and 53.43% to 75.51% for 2 MPa, owing to the increase in compression approximately by 41% from their base cases and it is also crucial to note that GDL compression exaggerates at higher clamping pressures. The misalignment results in the sagging of Membrane Electrode Assembly (MEA), and the amplitude of wave nature is proportional to the degree of misalignment and clamping pressure, indicating the misalignment is the sole factor for structural changes. As a result, considerable variance in current distribution and average value is observed, i.e., at operating voltage 0.5 V, the current density drops from 4472.7 to 4264.4, 4420.7 to 4211.8, and 4374.1 to 4161.3 A m−2 from cases 1 to 6 for clamping pressures 1, 1.5, and 2 MPa, respectively, resulting in a 4.7% loss in performance. According to the observations, a misalignment of 60% is tolerable, with minimal performance loss and negligible non-uniformity in cell distributions.