Extensive research has been conducted over the past few decades on carbon-free hydrogen energy. Hydrogen, being an abundant energy source, requires high-pressure compression for storage and transportation due to its low volumetric density. Mechanical and electrochemical compression are two common methods used to compress hydrogen under high pressure. Mechanical compressors can potentially cause contamination due to the lubricating oil when compressing hydrogen, whereas electrochemical hydrogen compressors (EHCs) can produce high-purity, high-pressure hydrogen without any moving parts. A study was conducted using a 3D single-channel EHC model focusing on the water content and area-specific resistance of the membrane under various temperature, relative humidity, and gas diffusion layer (GDL) porosity conditions. Numerical analysis demonstrated that the higher the operating temperature, the higher the water content in the membrane. This is because the saturation vapor pressure increases with higher temperatures. When dry hydrogen is supplied to a sufficiently humidified membrane, the actual water vapor pressure decreases, leading to an increase in the membrane’s area-specific resistance. Furthermore, with a low GDL porosity, the viscous resistance increases, hindering the smooth supply of humidified hydrogen to the membrane. Through a transient analysis of an EHC, favorable operating conditions for rapidly hydrating membranes were identified.