BACKGROUND To investigate the eye movement functions in children with amblyopia and recovered amblyopia by a binocular eye-tracking paradigm. METHODS Eye movements of 135 pediatric subjects (age range: 4-14 years), including 45 amblyopic children, 45 recovered amblyopic children and 45 age-similar normal controls, were recorded under binocular viewing with corrected refractive errors (if any). The deviation of gaze positions relative to the target location was recorded as the mean from both eyes. Main outcome measures included fixation deviations (degree) along horizontal and vertical axes in the sustained fixation test (Fix-X, Fix-Y) and visually guided saccade test (Sac-X, Sac-Y), which were compared across the three groups and between each two groups. RESULTS All the four deviations were significantly larger in the amblyopia group compared to the other two groups, indicating increased inaccuracy of sustained and post-saccadic fixations in amblyopia. However, there was no significant difference in deviations between recovered amblyopic children and normal controls. Repeated measures showed similar results overall and within each group. Mild to moderate amblyopes and severe amblyopes did not differ in the four deviations. No significant interaction was found between subject groups and clinical characteristics (age, refractive status, and anisometropia). CONCLUSIONS Amblyopic children have poor eye movement functions with increased inaccuracy of sustained and post-saccadic fixations, which appear to be restored in children with recovered amblyopia. Binocular assessment of eye movements provides valuable indicators of functional recovery in amblyopia.