Glioblastoma is one of the most malignant tumors with very poor prognosis. Glioma stem cells (GSCs) occupy a small proportion in glioma, but they are closely associated with radiotherapy and chemotherapy resistance, promoting tumor angiogenesis, hypoxia response, invasion and recurrence. Therefore, GSCs have become a new target for tumor treatment and are used in drug screening. Rupesin E is a natural compound obtained from Valeriana jatamansi, and its antitumor activity has not been reported. In the present study, the antitumor activity of rupesin E was investigated, and the results demonstrated that it inhibited the proliferation of GSCs (GSC-3#, GSC-12#, GSC-18#) with the IC 50 values of 7.13±1.41, 13.51±1.46 and 4.44±0.22 µg/ml, respectively. In addition, immunofluorescence cell staining and flow cytometry techniques demonstrated that rupesin E inhibited GSC proliferation and induced apoptosis. Furthermore, rupesin E inhibited the ability of GSC colony formation, indicating its antitumor activity against GSCs in vitro.