The effect of gas diffusion layer (GDL) compression on the polarization curves of a polymer electrolyte membrane fuel cell was analyzed using a polarization curve-fitting model. The polarization curves measured at four different GDL compression ratios were fitted with the model and were decomposed into an open circuit voltage and three over-voltages resulting from activation, ohmic, and mass-transport losses, respectively. The model fitting was excellent enough to use the model in the subsequent analysis of the GDL compression effect. The relationship between the over-voltages and the compression ratio was investigated by analyzing the estimated model parameters, and an optimal compression ratio was determined for the fuel cell. The proposed analysis method based on the polarization curve-fitting model can be applied to identifying quantitative differences of polarization curves under various operating conditions and designs for fuel cells.