Distributed networks of brain areas interact with one another in a time-varying fashion to enable complex cognitive and sensorimotor functions. Here we used new network-analysis algorithms to test the recruitment and integration of large-scale functional neural circuitry during learning. Using functional magnetic resonance imaging data acquired from healthy human participants, we investigated changes in the architecture of functional connectivity patterns that promote learning from initial training through mastery of a simple motor skill. Our results show that learning induces an autonomy of sensorimotor systems and that the release of cognitive control hubs in frontal and cingulate cortices predicts individual differences in the rate of learning on other days of practice. Our general statistical approach is applicable across other cognitive domains and provides a key to understanding time-resolved interactions between distributed neural circuits that enable task performance.