Regulation of microcirculation and other physiological processes have strong non-linear character and involves complex of different processes, every process with own hierarchy in time and different frequencies. Traditional Fourier analysis does not provide sufficient power and resolution to elucidate characteristic of low vasomotor frequencies. Therefore, we apply a Time–frequency (wavelet) analysis on the signal obtained by Laser Doppler flow meter (LDF) at 25 healthy volunteers, exposed at the same time to low frequency electromagnetic fields, used for physiotherapy. Signal processing include Matlab based algorithms for digital signal processing (DSP) and Matlab Spectral analysis toolbox of simultaneous registered variations in Blood Pressure (BP), Laser Doppler Flow (LDF), and Intravital microscopy (IVM). It provides useful information about regulatory mechanisms and vegetative nervous system regulation of peripheral blood flow. Continuous changes in blood pressure variations and perfusion of extremities were measured prior and after 10, 20, and 30 min ELF-EMF (10, 16, 20, and 30 mT), exposure. After wavelet analysis of the blood flow signals and vasomotion changes signals, several frequency bands were distinguished: 0.0095–0.02 Hz; (α), 0.02–0.06 Hz; (β), 0.06–0.15 Hz; (γ), 0.15–0.4 Hz; (δ), and 0.4–1 Hz; (θ) for LDF data and 0.0095–0.4 Hz; (α), 0.4–0.75 Hz; (β), 0.75–0.9 Hz; (γ), 0.9–1.2 Hz; (δ), and 1.2–2 Hz; (θ) for IVM data. In this study, overlapping of some frequency bands between IVM and LDF data were found. Overlapping of the frequency bands has two ways of interpretation, one related with similarity of the structures and tissues and other related with output of ELF-EMF stimulation. We used also correlation and cross-correlation analysis to compare non-invasive (BP measurements and LDF) data, with invasive intravital microscopy (IVM) data (obtained on animals in vivo), during ELF-EMF stimulation. IVM data were used as a reference value, for certain information of possible mechanisms of biological response at the tissue and blood vessel level after ELF-EMF exposure with frequency in the range from 10 to 50 Hz and magnetic flux density of 20 mT. Comparative analysis of IVM and LDF, frequency bands show that they have statistical significant changes after ELF-EMF stimulation. Five subintervals were confirmed (α-, β-, γ-, δ-, and θ). The findings indicate that local ELF-EMF exposure at the constant temperature of the media increases skin blood flow at the upper extremities which have a contribution to the α-frequency band at IVM.