Our knowledge of infant perception and cognition is primarily based on habituation and dishabituation, but the underlying neural mechanisms for these processes per se remain unclear. It has been argued that habituation is related to building internal representations of repeated stimuli in the central nervous system, whereas dishabituation is related to an increased attention to novel items and events. This leads to a hypothesis that a distributed network including the sensory, association and prefrontal cortical regions of young infants is involved in those processes, in contrast with the classical developmental view that onset of the functioning of the prefrontal cortex is delayed. Here we examined the time evolution of spatio-temporal hemodynamic responses related to the auditory habituation and dishabituation in the temporal and prefrontal regions of 3-month-old infants by using multichannel near-infrared spectroscopy. We found that the temporal regions remained activated by repetitive auditory stimuli; however, the prefrontal regions exhibited phasic activation in relation to novel stimuli. The dissociated activation pattern between the temporal and prefrontal regions suggests that distinct cortical regions play distinct functional roles in auditory habituation and dishabituation, and that the prefrontal cortex is involved in perceiving invariance or novelty of the immediate environment in early infancy.