In this systematic review and meta-analysis, we explore how the time scale of practice affects patterns of brain activity associated with motor skill acquisition. Fifty-eight studies that involved skill learning with healthy participants (117 contrasts) met inclusion criteria. Two meta-contrasts were coded: decreases: peak coordinates that showed decreases in brain activity over time; increases: peak coordinates that showed increases in activity over time. Studies were grouped by practice time scale: short (≤1 h; 25 studies), medium (>1 and ≤24 h; 18 studies), and long (>24 h to 5 weeks; 17 studies). Coordinates were analyzed using Activation Likelihood Estimation to show brain areas that were consistently activated for each contrast. Across time scales, consistent decreases in activity were shown in prefrontal and premotor cortex, the inferior parietal lobules, and the cerebellar cortex. Across the short and medium time scales there were consistent increases in supplementary and primary motor cortex and dentate nucleus. At the long time scale, increases were seen in posterior cingulate gyrus, primary motor cortex, putamen, and globus pallidus. Comparisons between time scales showed that increased activity in M1 at medium time scales was more spatially consistent across studies than increased activity in M1 at long time scales. Further, activity in the striatum (viz. putamen and globus pallidus) was consistently more rostral in the medium time scale and consistently more caudal in the long time scale. These data support neurophysiological models that posit that both a cortico-cerebellar system and a cortico-striatal system are active, but at different time points, during motor learning, and suggest there are associative/premotor and sensorimotor networks active within each system.