Glioblastoma multiforme (GBM) is among the most aggressive cancers, with substantial metastasis potential. Here, we investigated the impact of graphene oxide nanoparticles (NPs) conjugated with cyclodextrin-containing selenium on the apoptosis and metastasis of U87 cells. Different methods were used to assess the physiochemical properties of NPs. The cytotoxicity of NPs was evaluated using the MTT assay, and their effect on the apoptosis of U87 cells was determined by flow cytometry. We also measured the expression of apoptosis and metastasis-related genes, the reactive oxygen species (ROS) levels, and the migration ability of U87 cells treated with beta-cyclodextrin-graphene oxide nanoparticles (B-CD-GO-NPs) loaded with selenium. Se (B-CD-GO-NPs) possessed a favorable size and zeta potential. In U87 cells, Se (B-CD-GO-NPs) exhibited an IC50 of 50 μg/ml, while in normal fibroblast L929 cells no significant toxicity was observed at this concentration. Se (B-CD-GO-NPs) significantly increased p53 and Bax gene expression and decreased Bcl-2 gene expression. They also inhibited the migration ability of U87 cells by reducing the gene expression and activity of matrix metalloproteinases-2 (MMP-2) and MMP-9. Moreover, treatment with Se (B-CD-GO-NPs) significantly increased the intracellular ROS levels, the sub-G1 cell population, and apoptosis. Overall, the promising anticancer effects of Se (B-CD-GO-NPs) in U87 cells could have a good potential for the development of these nanoparticles in the future GBM treatment.Graphical Abstract: