This study investigates the use of empirical mode decomposition (EMD) to extract intrinsic mode functions (IMFs) for the spectral analysis of EEG signals in healthy individuals and its possible biological interpretations. Unlike traditional EEG analysis, this approach does not require the establishment of arbitrary band limits. The study uses a multivariate EMD algorithm (APIT-MEMD) to extract IMFs from the EEG signals of 34 healthy volunteers. The first six IMFs are analyzed using two different methods, based on FFT and HHT, and the results compared using the ANOVA test and the Bland–Altman method for agreement test. The outcomes show that the frequency values of the first six IMFs fall within the range of classic EEG bands (1.72–52.4 Hz). Although there was a lack of agreement in the mean weighted frequency values of the first three IMFs between the two methods (>3 Hz), both methods showed similar results for power spectral density (<5% normalized units, %, of power spectral density). The HHT method is found to have better frequency resolution than APIT-MEMD associated with FTT that produce less overlapping between IMF3 and 4 (p = 0.0046) and it is recommended for analyzing the spectral properties of IMFs. The study concludes that the HHT method could help to avoid the assumption of strict frequency band limits, and that the potential impact of EEG physiological phenomenon on mode-mixing interpretation, particularly for the alpha and theta ranges, must be considered in future research.