Novel sounds in the auditory oddball paradigm elicit a biphasic dilation of the pupil (PDR) and P3a as well as novelty P3 event-related potentials (ERPs). The biphasic PDR has been hypothesized to reflect the relaxation of the iris sphincter muscle due to parasympathetic inhibition and the constriction of the iris dilator muscle due to sympathetic activation. We measured the PDR and the P3 to neutral and to emotionally arousing negative novels in dark and moderate lighting conditions. By means of principal component analysis (PCA) of the PDR data we extracted two components: the early one was absent in darkness and, thus, presumably reflects parasympathetic inhibition, whereas the late component occurred in darkness and light and presumably reflects sympathetic activation. Importantly, only this sympathetic late component was enhanced for emotionally arousing (as compared to neutral) sounds supporting the hypothesis that emotional arousal specifically activates the sympathetic nervous system. In the ERPs we observed P3a and novelty P3 in response to novel sounds. Both components were enhanced for emotionally arousing (as compared to neutral) novels. Our results demonstrate that sympathetic and parasympathetic contributions to the PDR can be separated and link emotional arousal to sympathetic nervous system activation.