The suppression of neuronal responses to a repeated event is a ubiquitous phenomenon in neuroscience. However, the underlying mechanisms remain largely unexplored. The aim of this study was to examine the temporal evolution of experience-dependent changes in connectivity induced by repeated stimuli. We recorded event-related potentials (ERPs) during frequency changes of a repeating tone. Bayesian inversion of dynamic causal models (DCM) of ERPs revealed systematic repetition-dependent changes in both intrinsic and extrinsic connections, within a hierarchical cortical network. Critically, these changes occurred very quickly, over inter-stimulus intervals that implicate short-term synaptic plasticity. Furthermore, intrinsic (within-source) connections showed biphasic changes that were much faster than changes in extrinsic (between-source) connections, which decreased monotonically with repetition. This study shows that auditory perceptual learning is associated with repetition-dependent plasticity in the human brain. It is remarkable that distinct changes in intrinsic and extrinsic connections could be quantified so reliably and non-invasively using EEG.