Representing the leading cause of childhood cancer mortality, pediatric brain tumors are comprised of diverse histological features, genetic perturbations, cellular populations, treatment protocols, and clinical outcomes. In this chapter we discuss recent and emerging data that implicate cancer stem cells (also known as brain tumor-initiating cells) in initiating and maintaining the growth of a number of pediatric brain tumors including: medulloblastoma, supratentorial primitive neuroectodermal tumor, atypical teratoid/rhabdoid tumor, ependymoma, low-grade glioma, glioblastoma, diffuse intrinsic pontine glioma, germ cell tumor, and craniopharyngioma. The development of a stem cell framework for the study and treatment of these tumors will enable future clinical approaches to harness the heterogeneous cellular and genomic landscape of these solid tumors as an avenue for developing targeted patient-oriented therapies, thereby improving the overall survivorship for the most lethal childhood cancer.