A new approach for detection oscillatory patterns and estimation of their dynamics based by a modified CWT skeleton method is presented. The method opens up additional perspectives for the analysis of subtle changes in the oscillatory activity of complex nonstationary signals. The method was applied to analyze unique experimental signals obtained in usual conditions and after the non-invasive increase in the blood–brain barrier (BBB) permeability in 10 male Wistar rats. The results of the wavelet-analysis of electrocorticography (ECoG) recorded in a normal physiological state and after an increase in the BBB permeability of animals demonstrate significant changes between these states during wakefulness of animals and an essential smoothing of these differences during sleep. Sleep is closely related to the processes of observed changes in the BBB permeability.