Medulloblastoma, a tumor of the cerebellum, is the most common pediatric central nervous system malignancy. These tumors are etiologically linked to mutations in the Sonic hedgehog (Shh) pathway, which signals through the primary, non-motile cilium. The growth of these aggressive tumors relies on the self-renewal of tumor-propagating cells known as cancer stem cells (CSCs). Previous reports have implicated CD133-expressing cells as CSCs in brain tumors, while those expressing CD15 have been shown to propagate medulloblastoma. Here, we demonstrate that CD133₊ and CD15₊ cells are distinct medulloblastoma populations. CD15+ cells comprise approximately 0.5-1% of total human tumor cells, display CSC properties in culture and are detected in the Smoothened A1 transgenic mouse model of medulloblastoma. Additionally, we report on a medulloblastoma patient with enriched CD15₊ cells in recurrent vs. primary tumors. We also demonstrate that human medulloblastoma cells critically rely on the establishment of primary cilia to drive Shh-mediated cell division. Primary cilia are found in external granule cells of human fetal cerebellum and in 12/14 medulloblastoma samples. Yet, CD15₊ medulloblastoma cells lack primary cilia, suggesting that this CSC population signals independently of Shh signaling. These results are important when considering the effects of current and prospective treatment modalities on medulloblastoma CSC populations.