Top-down modulation is an essential cognitive component in human perception. Despite mounting evidence of top-down perceptual modulation in adults, it is largely unknown whether infants can engage in this cognitive function. Here, we examined top-down modulation of motion perception in 6- to 8-month-old infants (recruited in North America) via their smooth-pursuit eye movements. In four experiments, we demonstrated that infants’ perception of motion direction can be flexibly shaped by briefly learned predictive cues when no coherent motion is available. The current findings present a novel insight into infant perception and its development: Infant perceptual systems respond to predictive signals engendered from higher-level learning systems, leading to a flexible and context-dependent modulation of perception. This work also suggests that the infant brain is sophisticated, interconnected, and active when placed in a context in which it can learn and predict.