Based on the fundamental electrode theory and the impedance experimental study, a numerical model to simulate the low current distribution in the time domain and the electrochemical impedance spectra of the cathode catalyst layer (CCL) of polymer electrolyte fuel cells (PEFCs) has been developed in this study. The model development consists of two stages: to establish the fundamental equations for the low current distribution in the CCL in the time domain and to resolve the fundamental theory in the frequency domain. It was validated by comparing the simulated impedance of the CCL directly against the impedance data measured from an operational test cell. The simulated frequency response agrees well with the experimental data. The model was applied in the time domain to simulate the effects of the proton resistance and the double-layer capacitance across the CCL on the transitory and steady-state current distribution. The results showed that the model has established a backbone understanding of how the low current electrochemical mechanisms relate to the electrochemical impedance spectra of the CCL. It establishes a wider scope to relate the electrochemical impedance data to the fundamental theory of PEFCs.