An increasing number of studies within the recent years connected physical exercise with changes in brain cortical activity. Most of this data (1) refers to aerobic exercise and (2) does not correlate to psychological parameters although it is well known that exercise has a positive effect on mood. In times where health activities play a major role it is increasingly necessary to connect somato-physiological and somatopsychological components of physical activity. This study aimed to find changes in EEG activity and mood after low, preferred and high intensity running. EEG and actual state of mood were recorded before and after exercise. Results showed an effect for the preferred and high intensity velocity in both, EEG and mood. As only the higher frequency areas N18 Hz showed persisting decreases post-exercise we concluded that this might be a sign of outlasting effects of exercise on brain cortical activity which may have influences on general well-being. We could also show that there is a clear relationship between EEG activity and mood reflecting a basic principle of cortical excitation.