Gliomas are the most common type of brain tumor in the central nervous system of adults, and are highly aggressive, resistant to treatment, and prone to recurrence. Brain tumor stem cells (BTSCs) are implicated in tumor initiation and recurrence. Cluster of differentiation (CD)133 is currently the most widely used BTSC marker; however, its role in glioma development and progression is largely unknown. In this study, we evaluated CD133 expression in pairs of primary and recurrent human glioma specimens from 24 patients. We found that recurrent gliomas have aberrantly upregulated CD133 levels. To clarify the mechanism underlying this observation, we assessed CD133 promoter (P)2 methylation status by bisulfite sequencing and found that P2 hypomethylation was associated with the increase in CD133 expression and glioma recurrence. These results suggest that CD133 overexpression in BTSCs due to P2 hypomethylation underlies glioma recurrence, which may provide insight into the mechanism of glioma recurrence and provide a basis for novel therapies for glioma treatment.