Cancer stem cells (CSCs) are believed to be responsible for tumor metastasis, recurrence, and high mortality of cancer patients due to their high tumorigenicity resistance to chemo-radiotherapy. Morusin possesses anti-cancer activity through attenuation of NF-κB activity, which is up-regulated in cancer stem cells. The purpose of this study is to confirm the growth and migration inhibition effect of morusin on human cervical CSCs, and to clarify its partial mechanism of activity. Human cervical CSCs were enriched using non-adhesive culture system. Their stemness characteristics were identified with tumor sphere formation, self-renewal, toluidine blue staining, migration assays, RT-PCR analysis, and immunofluorescence staining of putative stem cell markers, Oct4, SOX2, and ALDH1; the epithelial-to-mesenchymal (EMT) transition markers and relevant transcription factors were evaluated with Western blotting. The growth and migration inhibition effects of morusin on human cervical CSCs were tested by cell proliferation, tumor sphere formation, and transwell assay; apoptotic death of human cervical CSCs in response to morusin was measured with DAPI staining, apoptotic DNA fragmentation; NF-κBp65, Bcl-2, Bax, and caspase-3 protein expressions were detected through Western blotting. Under this non-adhesive culture system, typical tumor spheres appeared within 5-7 days, the tumor sphere formation, self-renewal, and cell migration, expressions of putative stem cell markers, EMT markers, and relevant transcription factors of the tumor sphere cells were increased significantly. After morusin treatment, the proliferation, tumor sphere formation, and migration of human cervical CSCs were decreased significantly, DAPI-stained apoptotic cells increased, apoptotic DNA fragmentations formed evidently; the expression levels of NF-κBp65 and Bcl-2 decreased significantly, Bax, and caspase-3 increased significantly in a dose-dependent manner. Using the non-adhesive culture system, human cervical CSCs were enriched and expanded. Morusin has the potential to target and kill CSCs, and can inhibit human cervical growth and migration through NF-κB attenuation mediated apoptosis induction.