Objective: To investigate the effect of miR-206 on proliferation and metastasis of human nasopharyngeal carcinoma CNE2 cells, and to analyze the role of cyclin-dependent kinase 9 (CDK9). Methods: Expression levels of miR-206 in nasopharyngeal epithelial NP69 cells and human nasopharyngeal carcinoma CNE2 cells were detected by real-time quantitative polymerase chain reaction (RT-qPCR). The mimic and control of miR-206 were introduced into CNE2 cells, respectively. CCK-8 assay, Annexin V-FITC/PIstaining, clone formation assay, transwell migration assay and transwell invasion assay were used to evaluate the effect of miR-206 over-expression on cell viability, apoptosis, colony formation, migration and invasion in CNE2 cells, respectively. Finally, Expression levels of CDK9 in CNE2 cells and NP69 cells were detected by Western blot. The effect over-expression of CDK9 on migration and invasion in over-expression of miR-206 of CNE2 cells was further detected. Results: MiR-206 was lower expression in CNE2 cells. Over-expression of miR-206 decreased cell viability, colony formation, migration and invasion and induced apoptosis in CNE2 cells. CDK9 was higher expression in CNE2 cells. Over-expression of miR-206 inhibited Expression of CDK9 in CNE2 cells. However, over-expression of CDK9 could reverse the inhibitory effect of over-expression of miR-206 on the invasion and migration of CNE2 cells. Conclusion: MiRNA-206 inhibits the growth and metastasis in CNE2 cells, which may be mediated though inhibiting Expression of CDK9.