Amblyopia and strabismus are neurodevelopmental disorders often associated with impaired visual acuity and abnormal fixation eye movements (FEMs), including fixation instability and nystagmus. This study evaluated binocular and monocular visual acuity, fixation stability, and nystagmus waveforms in a large cohort of subjects with anisometropic, strabismic, and mixed amblyopia, strabismus without amblyopia, and controls. Using high-resolution eye tracking, we quantified fixation instability via the bivariate contour ellipse area (BCEA) and categorized FEMs into no nystagmus, fusion maldevelopment nystagmus (FMN), and other nystagmus types. Subjects with amblyopia demonstrated significant visual acuity deficits in both amblyopic and fellow eyes, with the most severe impairments seen in those with nystagmus. These findings underscore the multifactorial nature of visual impairment in amblyopia and strabismus, emphasizing the importance of considering both sensory and oculomotor contributions. Eye movement characteristics, such as fixation instability and nystagmus, may serve as key biomarkers for functional vision outcomes in these populations.