BackgroundSandhoff disease (SD) is a rare neurological disease with high clinical heterogeneity. SD in juvenile form is much rarer and it is often misdiagnosed in clinics. Therein, it is necessary to provide more cases and review the literature on juvenile onset SD.Case presentationA 14 years-old boy with eight years of walking difficulties, and was ever misdiagnosed as spinocerebellar ataxia. We found this patient after genetic testing carried rs201580118 and a novel gross deletion inHEXB(g.74012742_74052694del). Through review the literature, we found that was the first gross deletion identified at the 3’end ofHEXB, associated with juvenile onset SD from China.ConclusionThis case expanded our knowledge about the genotype and phenotype correlations in SD. Comprehensive genetic testing is important for the diagnosis of unexplained ataxia.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12883-023-03267-7.