Variation of brain dynamics under Zen meditation has been one of our major research interests for years. One issue encountered is the inaccessibility to the actual meditation level or stage as a reference. In this paper, we propose an alternative strategy for investigating the human brain in response to external flash stimuli during Zen meditation course. To secure a consistent condition of the brain dynamics when applying stimulation, we designed a recording of flash visual evoked potentials (F-VEPs) based on a constant background EEG (electroencephalograph) frontal $alpha-rhythm$ dominating activities that increase significantly during Zen meditation. Thus the flash-light stimulus was to be applied upon emergence of the frontal $alpha-rhythm$. The alpha-dependent F-VEPs were then employed to inspect the effect of Zen meditation on brain dynamics. Based on the experimental protocol proposed, considerable differences between experimental and control groups were obtained. Our results showed that amplitudes of P1-N2 and N2-P2 on Cz and Fz increased significantly during meditation, contrary to the F-VEPs of control group at rest. We thus suggest that Zen meditation results in acute response on primary visual cortex and the associated parts.