The purpose of this work was to determine, in the Wistar male rats, the role of the stress system in the control of cerebral hemodynamics induced by emotional stress (air jet). Blood flow rates in the internal carotid arteries have been obtained using chronically implanted Doppler probes. In this investigation, air-jet stress provokes a rapid and substantial elevation of blood pressure combined with hyperemia and vasodilation. Spectral analysis reveals an increase in the variability of carotid blood flow and carotid vascular conductance during stress compared to the baseline state. The coherence between the two carotid blood flow, which provides a linear correlation index in the frequency domain, was calculated before (ordinary coherence) and after mathematical elimination of the influence of blood pressure (partial coherence). The main advantages of the technique are as follows:• It allows the measurement of cerebral blood flow while comparing them with the physiological parameters of the animal such as blood pressure.• Air-jet stress is a psychological rather than physical stress that generates hyperemia in a non-pharmacological way (no side effects) without injuring the animal or damaging the experimental installation during the recording sessions.• A simple method for tracing a kinetic path before and at the moment of stress initiation.• The presence of a catheter facilitates the administration of drug substances if required.• Laboratory-developed software, based on the Lab VIEW 5.1, allows real-time monitoring of blood pressure and carotid flow rates signals using fast Fourier transform.