Inhibition of both the de novo (DNP) and salvage (NSP) pathways of nucleoside synthesis has been demonstrated to impair leukemia cells. We endeavored to determine if this approach would be efficacious in glioblastoma (GBM). To diminish nucleoside biosynthesis, we utilized compound DI-39 that selectively targets NSP, in combination with thymidine (dT) that selectively targets DNP. We employed in vitro and ex vivo models to determine the effects of pre-treatment with dT +DI-39 on brain tumor stem cells (BTSC). Here, we demonstrate that this combinatorial therapy elicits a differential response across a spectrum of human patient derived GBM cultures. As determined by apoptotic markers, most cultures were relatively resistant to treatment, although a subset was highly sensitive. Sensitivity was unrelated to S-phase delay and to DNA damage induced by treatment. Bioinformatics analysis indicated that response across cultures was associated with the transcription factor PAX3 (associated with resistance) and with canonical pathways including the nucleotide excision repair pathway, PTEN (associated with resistance), PI3K/AKT (associated with sensitivity), and ErbB2-ErbB3. Our in vitro assays demonstrated that, in sensitive cultures, clonal sphere formation was reduced upon removal from pre-treatment. In contrast, in a resistant culture, clonal sphere formation was slightly increased upon removal from pre-treatment. Moreover, in an intracranial xenograft model, pre-treatment of a sensitive culture caused significantly smaller and fewer tumors. In a resistant culture, tumors were equivalent irrespective of pre-treatment. These results indicate that, in the subset of sensitive GBM, BTSC are targeted by inhibition of pyrimidine synthesis.