CLN3 disease, or juvenile Batten disease, is a neurodegenerative lysosomal storage disorder in which visual impairment is typically the earliest clinical manifestation. Although retinal pathology has been extensively studied, functional alterations within central visual pathways remain poorly understood. Here, we used functional ultrasound (fUS) imaging to characterize visually evoked activity across central visual circuits in young Cln3 knockout (Cln3-/-) mice before the onset of severe retinal degeneration. Visually evoked hemodynamic responses were quantified in regions spanning the geniculostriate and extrageniculate visual pathways, including cortical, thalamic, and midbrain regions. Regional pathological burden was assessed by immunohistochemical quantification of subunit c of mitochondrial ATP synthase (SCMAS), a hallmark pathological marker of CLN3 disease. Young Cln3-/- mice exhibited pathway-specific reorganization of visually evoked responses, with enhanced fUS activation in the extrageniculate pathway, including the midbrain, posterior thalamus, and anterior secondary visual cortex, whereas activation in the geniculostriate pathway was reduced in the anterior thalamus and preserved in the visual cortex relative to wild-type controls. SCMAS accumulation was increased across all examined visual regions but was greater in geniculostriate than extrageniculate regions, indicating differential regional vulnerability. Together, these findings identify early pathway-specific reorganization of central visual circuits before overt neurodegeneration and establish fUS imaging, combined with quantitative histopathology, as a promising approach for early detection and longitudinal monitoring of central nervous system dysfunction in CLN3 disease and related lysosomal storage disorders.