Learning to be skillful is an endowed talent of humans, but neural mechanisms underlying behavioral improvement remain largely unknown. Some studies have reported that the mean magnitude of neural activation is increased after learning, whereas others have instead shown decreased activation. In this study, we used functional magnetic resonance imaging (fMRI) to investigate learning-induced changes in the neural activation in the human brain with a classic motor training task. Specifically, instead of comparing the mean magnitudes of activation before and after training, we analyzed the learning-induced changes in multi-voxel spatial patterns of neural activation. We observed that the stability of the activation patterns, or the similarity of the activation patterns between the even and odd runs of the fMRI scans, was significantly increased in the primary motor cortex (M1) after training. By contrast, the mean magnitude of neural activation remained unchanged. Therefore, our study suggests that learning shapes the brain by increasing the stability of the activation patterns, therefore providing a new perspective in understanding the neural mechanisms underlying learning.