Visual perceptual learning (VPL) refers to a long-term improvement of visual task performance through training or experience, reflecting brain plasticity even in adults. In human subjects, VPL has been mostly studied using functional magnetic resonance imaging (fMRI). However, due to the low temporal resolution of fMRI, how VPL affects the time course of visual information processing is largely unknown. To address this issue, we trained human subjects to perform a visual motion direction discrimination task. Their behavioral performance and magnetoencephalography (MEG) signals responding to the motion stimuli were measured before, immediately after, and two weeks after training. Training induced a long-lasting behavioral improvement for the trained direction. Based on the MEG signals from occipital sensors, we found that, for the trained motion direction, VPL increased the motion direction decoding accuracy, reduced the motion direction decoding latency, enhanced the direction-selective channel response, and narrowed the tuning profile. Following the MEG source reconstruction, we showed that VPL enhanced the cortical response in early visual cortex (EVC) and strengthened the feedforward connection from EVC to V3A. These VPL-induced neural changes co-occurred in 160–230 ms after stimulus onset. Complementary to previous fMRI findings on VPL, this study provides a comprehensive description on the neural mechanisms of visual motion perceptual learning from a temporal perspective and reveals how VPL shapes the time course of visual motion processing in the adult human brain.