Accumulating evidence indicates that cancer stem cells(CSCs) are a source of resistance to radiation therapy(RT); however, the mechanism of this resistance remains unclear. 2-Methoxyestradiol (2-ME2) is a metabolic product of estrogen in the body. Recent studies have found that 2-ME2 regulates the activation of transcription factors, including nuclear factor (NF)-κB/hypoxia-inducible factor-1(HIF-1), thus contributing to tumor cell apoptosis and chemosensitivity. Therefore, 2-ME2 is being studied as a potential anticancer drug. The purpose of this study was to determine the effect and mechanism by which 2-ME2 inhibits nasopharyngeal carcinoma CNE-2 stem-like cell(NPCSC) proliferation and migration and reduces NPCSC radioresistance. This study has important significance for reducing the radioresistance of these cells to improve the cure rate of NPC. First, the NPCSCs were collected in a serum-free culture system and then identified by relevant experiments. The NPCSCs were treated with 2-ME2 (0-8µM) combined with X-ray exposure and Cell Counting Kit-8(CCK-8), Transwell assay, colony formation assay, western blot analysis, RT-PCR, flow cytometry and RNA interference technology were used to explore the effect and mechanism of 2-ME2 on NPCSCs. The results showed that the microspheres collected in the serum‑free culture system possessed CSC traits and radioresistance. 2-ME2 obviously inhibited NPCSC growth and migration and reduced NPCSC radioresistance. 2-ME2 decreased NF-κB p65 and HIF-1α protein expression, downregulated NF-κB p65 nuclear localization, and reversed epithelial-mesenchymal transition(EMT). NF-κB p65 knockdown reduced HIF-1α expression, reversed EMT, and enhanced the suppressive effect of 2-ME2 on NPCSCs. Collectively, these data indicate that 2-ME2 inhibits NPCSC proliferation and migration and reduces the radioresistance of NPCSCs via NF-κB/HIF-1 signaling pathway inactivation and EMT reversal.