In this study, wavelet transforms and FFT methods, which transform method is better for spectral analysis of the brain signals are investigated. Statistical and Fourier methods are traditional techniques and tools to analyze time series signals in general, including biomedical data. In this paper as spectral analysis tools, wavelet transform and harmonic transform are used. Both transform methods are applied to electroencephalogram (EEG) of a possibly epilepsy patient and are compared. For this purpose in the harmonic transform case, the variations of first-sixth-order harmonic amplitudes and phases provide a useful tool of understanding the large- and local-scale effects on the parameters. Moreover, temporal and frequency variations of variables are also detected by wavelet transforms. The results of this study are compared with previous studies. The comparison of results show that the wavelet transform method has more advantage in detecting brain diseases.