Dysfunctional emotion processing is a key aspect of many neuropsychiatric disorders. This dysfunction may be due to an abnormal magnitude of neural substrate activation during emotion processing or due to an altered time course of the neural substrate response. To better understand the temporal characteristics of the neural substrate activation underlying implicit emotion processing, nine healthy female controls were repeatedly exposed to pictures of affective faces while performing a gender identification task in an fMRI. As the salience of the stimuli decreased with repeated exposure, brain areas implicated in a right hemispheric spatial attention network (including the posterior parietal cortex (BA 40) and the frontal eye fields (BA 6)) habituated while brain areas lateralized to the left hemisphere (including the angular gyrus (BA 39), posterior superior temporal gyrus (BA 39) and insula (BA 13)) sensitized. These results provide strong evidence that the time course of activation is a critical component when assessing the function of neural substrates underlying emotion processing (specifically whether habituation is altered) in neuro-psychiatric patients.