Background Glioblastoma (GBM) is a highly aggressive tumor with unmet therapeutic needs, which can be explained by extensive intra-tumoral heterogeneity and plasticity. In this study, we aimed to investigate the specific metabolic features of Glioblastoma stem cells (GSC), a rare tumor subpopulation involved in tumor growth and therapy resistance. Methods We conducted comprehensive analyses of primary patient-derived GBM cultures and GSC-enriched cultures of human GBM cell lines using state-of-the-art molecular, metabolic and phenotypic studies. Results We showed that GSC-enriched cultures display distinct glycolytic profiles compared with differentiated tumor cells. Further analysis revealed that GSC relies on pyruvate carboxylase activity for survival and self-renewal capacity. Interestingly, inhibition of pyruvate carboxylase led to GSC death, particularly when the glutamine pool was low, and increased differentiation. Finally, while GSC displayed resistance to the chemotherapy drug etoposide, genetic or pharmacological inhibition of pyruvate carboxylase restored etoposide sensitivity in GSC, both in vitro and in orthotopic murine models. Conclusion Our findings demonstrate the critical role of pyruvate carboxylase in GSC metabolism, survival and escape to etoposide. They also highlight pyruvate carboxylase as a therapeutic target to overcome therapy resistance in GBM.