Membrane electrode assembly (MEA) buckling tests in microscopic clearances under humidity cycles and numerical analyses by finite element method (FEM) were conducted. The NR211 (Dupont, 25-μm thickness, equivalent weight (EW) = 1100) sandwiched between catalyst layers (CLs) was used as the MEA. Based on tensile tests of the NR211 and NR211-CL and FEM simulation of tensile tests, the Young’s modulus and yield point of CL were estimated. While the CL had a higher Young’s modulus than the NR211 in water vapor, the CL indicated a lower Young’s modulus than the NR211 in liquid water at 80 °C. The buckling tests in microscopic diameter of 200 μm in polyimide film were carried out. The heights of bulge in the NR211 and NR211-CL after five humidity cycles were measured with a laser microscope. The height of the NR211-CL was lower than that of the NR211, due to the stiffer CL and the lower swelling ratio of the NR211-CL. Moreover, when the humidity cycles were repeated less than 1000 times, cracks were formed in the CL. The stress-strain behaviors of the NR211-CL buckling test under a humidity cycle were investigated by using the FEM. When the NR211-CL swelled, higher stress was developed at the topside of bulge and topside of bulge round. These portions corresponded to the CL crack-formed portions in the buckling test. When the NR211-CL deswelled, the tensile stress was induced in the entire NR211. The mechanical degradation mechanisms were considered as follows: Firstly, cracks initiate and propagate in the CL when the MEA swells in repeating humidity cycles. Moreover, the tensile stress is induced in the polymer electrolyte membrane (PEM) under deswelling and the CL cracks propagate into the PEM from the CL, which results in pinholes in the PEM.