Single cell gene expression profiling of pediatric central nervous system (CNS) tumors holds great potential to further our understanding of carcinogenesis, augment prognostic indicators, and identify rational therapeutic targets. Whereas the genomic characteristics of these tumors are fairly well-defined in aggregate, the extent to which cellular heterogeneity is associated with carcinogenesis and clinical outcomes is largely unknown. Here we profile single nuclei gene expression in 36 brain tumor specimens from individuals with a diagnosis of ependymoma, glioma, or embryonal CNS tumor with substantial follow up time, as well as non-tumor brain tissue from three pediatric controls. We used the 10X Genomics Single Cell platform to obtain single nuclei for RNA sequencing in conjunction with bulk RNA sequencing. In conjunction with this study, we obtained 5-methyl- and 5-hydroxymethylation profiles on these samples to investigate functional aspects of gene regulation by cytosine modification. The data and results from this study are expected to reveal an abundance of information about pediatric CNS tumors with value for the broader scientific community.