A method for dynamic cerebral autoregulation (CA) assessment includes acquiring a blood pressure (BP) signal having a first oscillatory pattern from a first individual, acquiring a blood flow velocity (BFV) signal having a second oscillatory pattern from the first individual, decomposing the BP signal into a first group of intrinsic mode functions (IMFs), decomposing the BFV signal into a second group of IMFs, determining dominant oscillatory frequencies in the first group of IMFs, automatically selecting a first characteristic IMF from the first group of IMFs that has its associated dominant oscillatory frequency in a predetermined frequency range, automatically selecting a second characteristic IMF from the second group of IMFs, calculating a time sequence of instantaneous phase difference between the first characteristic IMF and the second characteristic IMF, computing an average of the instantaneous phase difference in the time sequence, and identifying a pathological condition in the first individual.