Learning the timing of rapidly changing sensory events is crucial to construct a reliable representation of the environment and to efficiently control behavior. The neurophysiological mechanisms underlying the learning of time are unknown. We used functional and structural magnetic resonance imaging to investigate neurophysiological changes and individual brain differences underlying the learning of time in the millisecond range. We found that the representation of a trained visual temporal interval was associated with functional and structural changes in a sensory-motor network including occipital, parietal, and insular cortices, plus the cerebellum. We show that both types of neurophysiological changes correlated with changes of performance accuracy and that activity and gray-matter volume of sensorimotor cortices predicted individual learning abilities. These findings represent neurophysiological evidence of functional and structural plasticity associated with the learning of time in humans and highlight the role of sensory-motor circuits in the perceptual representation of time in the millisecond range.