Despite the fact that emotions involve multiple time-varying components, little is known about the underlying neural basis of these temporal dynamics. In this paper, we assess these temporal dynamics by using time-varying hemodynamic response functions (HRF) to model BOLD responses to emotional stimuli. We show that these time-varying HRFs lead to a better fit to the BOLD data and yield larger areas of significant activation than do conventional gamma-based canonical HRFs. We also report for the first time that intensity of emotional experience is associated with both magnitude and duration of brain activation. Specifically, greater negative emotional intensity was associated with greater magnitude of activation in the occipital cortex and with longer duration of activation in regions along the cortical midline associated with self-referent processing: the anterior medial prefrontal cortex and the posterior cingulate cortex. These data significantly advance our understanding of how the brain processes emotion and suggest that the intensity of a negative emotional experience is due in part to elaborative self-referent processing that is captured by the duration of neural activity in cortical midline structures. These data also underscore the importance of using modeling techniques that will help elucidate the chronometry of both normal and psychopathological emotional processes.