BackgroundCLN3 disease is a major cause of childhood neurodegeneration. Onset of visual failure around 6 years of age is thought to precede cognitive deterioration by a few years, but casuistic reports question this paradigm. The aim of our study is to delineate timing of cognitive decline in CLN3 disease.MethodsEarly neurocognitive functioning in CLN3 disease was analyzed using age at onset of visual and cognitive decline and IQ scores from literature-derived patient descriptions, supplemented with IQ scores and school history from a retrospective referral center cohort. We analyzed protracted and classical CLN3 separately and added a control group of patients diagnosed with juvenile onset macular degeneration (early onset Stargardt disease) to control for possible effects of rapid vision loss on neurocognitive functioning.ResultsOnset of cognitive decline at a mean age of 6.8 years (range 2–13 years, n = 19) paralleled onset of visual deterioration at a mean age of 6.4 years (range 4–9 years, n = 81) as supported by an early decline in IQ scores in classical CLN3 disease. Onset and course of vision loss was similar in patients with protracted CLN3. The decreased IQ levels at diagnosis (mean 68.4, range 57–79, n = 9) in the referral cohort were consistently associated with an aberrant early school history contrasting normal school history and cognition in Stargardt disease patients.ConclusionsCognitive dysfunction is universally present around diagnosis in classical CLN3 disease.Electronic supplementary materialThe online version of this article (10.1007/s10545-018-0143-x) contains supplementary material, which is available to authorized users.