Perceptual learning is regarded as a manifestation of experience-dependent plasticity in the sensory systems, yet the underlying neural mechanisms remain unclear. We measured the dynamics of performance on a visual task and brain activation in the human primary visual cortex (V1) across the time course of perceptual learning. Within the first few weeks of training, brain activation in a V1 subregion corresponding to the trained visual field quadrant and task performance both increased. However, while performance levels then saturated and were maintained at a constant level, brain activation in the corresponding areas decreased to the level observed before training. These findings indicate that there are distinct temporal phases in the time course of perceptual learning, related to differential dynamics of BOLD activity in visual cortex.