The purpose of this study was to unveil temporal relationship of physiological states during emotional experience. It has been widely accepted that emotion arises from interaction between cerebral processing and bodily response (i.e., autonomic nervous system: ANS). Therefore, we measured indices of both types of activities, using frontal alpha asymmetry (Davidson, Ekman, Saron, Senulis, & Friesen, 1990) for cerebral processing, and heart rate (HR) for ANS. Twenty-two participants watched six video clips for emotion induction (two each for negative, neutral, and positive emotions), during which electroencephalograms (EEGs) and electrocardiograms (ECGs) were recorded. Cross-correlation analyses revealed that the fluctuation of frontal alpha asymmetry synchronized with that of HR only when participants watched positive video clips. Because most participants changed their facial expression during the clips, it is possible that facial expression was induced by the synchronization of frontal alpha asymmetry and ANS activity. In addition, when they watched one of the positive clips, frontal alpha asymmetry fluctuation was preceded by HR variation. This indicated that ANS response might influence activity of cerebral area where frontal alpha asymmetry arises.