Neuronal ceroid lipofuscinoses (NCLs) are a group of disorders characterized by neurodegeneration and intracellular accumulation of an auto-fluorescent lipopigment. Together, NCLs represent the most common cause of neurodegeneration in children. The juvenile form (JNCL), due to mutations in CLN3, is characterized by progressive vision loss, epilepsy, dementia, behavioral difficulties, and motor impairment. The goal of this study was to develop a staging system for JNCL to facilitate stratification by clinical disease severity in future research. Data from the University of Rochester Batten Center NCL natural history database were analyzed using cross-sectional and longitudinal methods with Prism 7. The characteristic symptoms of JNCL were used to define four clinical stages: Stage 1 - isolated loss of vision; Stage 2 - loss of vision plus seizures; Stage 3 - loss of independent activities of daily living; Stage 4 - loss of independent walking. Significant differences in mean age (years) were found between Stage 1 and Stage 2 [3.196 (95% CI:1.48-4.91); p <0.0001] and Stage 3 and Stage 4 [4.301 (95% CI:2.83-5.77); p<0.001]. There was no significant difference between Stage 2 vs. Stage 3 [1.27 (95% CI:0.19-2.73); p = 0.15]. Based on the lack of difference between Stage 2 and Stage 3, Stage 3 was redefined as loss of independent walking and Stage 4 was eliminated. A 3-stage system can be used to categorize the progression of JNCL disease as a function of age and has the potential to guide primary and secondary endpoints in future clinical trials.