Recent studies have revealed rapid (e.g., hours to days) training-induced cortical structural changes using magnetic resonance imaging (MRI). Currently, there is great interest in studying how such a rapid brain structural change affects behavioral improvement. Structural reorganization contributes to memory or enhanced information processing in the brain and may increase its capability of skill learning. If the gray matter (GM) is capable of such rapid structural reorganization upon training, the extent of volume increase may characterize the learning process. To shed light on this issue, we conducted a case series study of 5-day visuomotor learning using neuroanatomical imaging, and analyzed the effect of rapid brain structural change on motor performance improvement via regression analysis. Participants performed an upper-arm reaching task under left-right mirror-reversal for five consecutive days; T1-weighted MR imaging was performed before training, after the first and fifth days, and 1 week and 1 month after training. We detected increase in GM volume on the first day (i.e., a few hours after the first training session) in the primary motor cortex (M1), primary sensory cortex (S1), and in the hippocampal areas. Notably, regression analysis revealed that individual differences in such short-term increases were associated with the learning levels after 5 days of training. These results suggest that GM structural changes are not simply a footprint of previous motor learning but have some relationship with future motor learning. In conclusion, the present study provides new insight into the role of structural changes in causing functional changes during motor learning.