Square-wave stimulation used in modulation excitation spectroscopy [D. Baurecht, U.P. Fringeli, Rev. Sci. Instrum. 72 (2001) 3782] can have significant advantages over a simple sinusoidal-wave due to the high odd-frequency terms contained in square-wave, particularly when a system response is close to linear. Phase-sensitive detection (PSD) affords separating the signals of the different frequency terms with a high signal-to-noise ratio by averaging a number of modulation cycles. A modulation excitation experiment applying square-wave stimulation provides the same information as several experiments applying sinusoidal-wave stimulations at the same frequency as the square-wave stimulation and at higher frequencies. The amplitude and the phase lag of a response obtained by PSD at fundamental and higher frequencies using square-wave stimulation are related to the ones obtained by sinusoidal-wave stimulation using transfer function of a general system. Mixing property of a PM-IRRAS (polarization–modulation infrared reflection–absorption spectroscopy) flow-through cell was studied by a simple mixing tank model using square-wave concentration stimulation. The advantages of square-wave stimulation are shown by the characterization of the mixing property.