We consider the brain as an autonomous stochastic system, whose fundamental frequencies are locked to an external periodic stimulation. Taking into account that phase synchronization between brain response and stimulating signal is affected by noise, we propose a novel method for experimental estimation of brain noise by analyzing neurophysiological activity during perception of flickering visual stimuli. Using magnetoencephalography (MEG) we evaluate steady-state visual evoked fields (SSVEF) in the occipital cortex when subjects observe a square image with modulated brightness. Then, we calculate the probability distribution of the SSVEF phase fluctuations and compute its kurtosis. The higher kurtosis, the better the phase synchronization. Since kurtosis characterizes the distribution’s sharpness, we associate inverse kurtosis with brain noise which broadens this distribution. We found that the majority of subjects exhibited leptokurtic kurtosis (K > 3) with tails approaching zero more slowly than Gaussian. The results of this work may be useful for the development of efficient and accurate brain-computer interfaces to be adapted to individual features of every subject in accordance with his/her brain noise.