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In this paper, a frequency domain approach is proposed to measure the light flicker of the electricity transmission systems where the system frequency deviates significantly. Analytical expressions of the instantaneous light flicker sensation are obtained beginning from a voltage waveform and these expressions are used to obtain a flicker estimation method based on the IEC flickermeter. In the proposed method, the leakage effect of the FFT algorithm due to fundamental frequency variation is reduced by employing a spectral amplitude correction around the fundamental frequency. The eye-brain weighting curve is realised comparing the voltage spectrum with the tabulated normalised IEC flickermeter responses for sinusoidal voltage fluctuations of the IEC standard. The proposed method is tested on both simulated data and field data obtained from a power system. The comparison with the digital realization of the IEC flickermeter shows that the method gives satisfactory estimations with low computational complexity. The method is especially useful for conditions such as disturbances and subsequent system transients where the system frequency deviates, since it avoids the need for online sampling rate adjustment to prevent the leakage effect of the FFT.