Sanfilippo syndrome type B (Mucopolysaccharidosis type IIIB or MPS IIIB) is a recessive genetic disorder that severely affects the brain due to a deficiency in the enzyme α-N-acetylglucosaminidase (NAGLU), leading to intralysosomal accumulation of partially degraded heparan sulfate. There are no effective treatments for this disorder. In this project, we carried out an ex vivo lentiviral correction of neural stem cells derived from Naglu−/− mice (iNSCs) using a modified enzyme in which the NAGLU is fused to an Insulin-like Growth Factor II receptor (IGFIIR) binding peptide in order to improve the cross-correction efficiency. After brain transplantation of these corrected iNSCs into Naglu−/− mice and long-term evaluation of the cross-correction, we successfully detected NAGLU-IGFII activity in all transplanted animals, as well as decreased lysosomal accumulation and reduced astrocytic and microglial activation throughout the transplanted brain. In addition, we identified a novel neuropathological phenotype in untreated brains characterized by decreased levels of MAP2 protein and accumulation of synaptophysin-positive aggregates in the brain. Following transplantation, this Naglu−/− -specific phenotype was altered with restored levels of MAP2 expression and significantly reduced formation of synaptophysin-positive aggregates. Our results demonstrate the feasibility and long-term benefit of genetically corrected iNSCs transplantation in the Sanfilippo B brain and effective cross-correction of Sanfilippo-associated pathology in Naglu−/− mice. Our findings suggest that genetically engineered iNSCs can be used to effectively deliver the missing enzyme to the brain and treat Sanfilippo type B-associated neuropathology.