Microsaccades, incessant “fixational eye movements” (< 1°), are an important window into cognitive functions. Yet, its role in visual perceptual learning (VPL)–improvements in visual discrimination due to practice–remains practically unexplored. Here we investigated whether and how microsaccades change in VPL. Human observers performed a Landolt acuity task for 5 consecutive days and were assigned to the Neutral or Attention group. On each trial, two peripheral Landolt squares were presented briefly along a diagonal. Observers reported the gap side of the target stimulus. Training improved acuity and modified the microsaccade rate; with training, the rate decreased during the fixation period but increased during the response cue. Furthermore, microsaccade direction during the response cue was biased toward the target location, and training enhanced and sped up this bias. Finally, the microsaccade rate during a task-free fixation period correlated with observers’ initial acuity threshold, indicating that the fewer the microsaccades during fixation the better the individual visual acuity. All these results, which were similar for both the Neutral and Attention groups and at both trained and untrained locations, suggest that microsaccades could serve as a physiological marker reflecting functional dynamics in human perceptual learning.