Ataxia-telangiectasia (A-T) is a devastating and rare autosomal recessive neurodegenerative disease. It is characterised by progressive neurological pathology, among other symptoms, and caused by mutations in the ataxia-telangiectasia mutated (ATM) gene. The molecular mechanisms underlying the disease are poorly understood, partly due to a lack of appropriate animal and cellular models. Here, we use human tissue and Cerevance’s proprietary Nuclear Enriched Transcript Sort sequencing (NETSseq) platform to produce deep RNA-sequencing expression profiles (>12000 genes) of purified CNS cell types. Cerebellar tissue was donated by fourteen A-T and forty-one control donors, with no known CNS disease, and differential expression analysis was conducted. Cell-type specific transcriptomic profiles from 8 neuronal and glial cell types was achieved. Astrocytes produced the greatest number of differentially expressed genes (p<0.05) and Gene Set Enrichment Analysis (GSEA) showed that changes in gene sets involved in inflammation and immune response were heavily represented, suggesting an increase in astrocyte reactivity. These data provide transcriptional profiling of targeted cell types from A-T cerebellum using NETSseq, demonstrating cell type-specific pathways that may be altered in disease and providing insights into molecular mechanisms and potential future drug targets.