Dysregulation of microRNAs has been demonstrated to contribute to malignant progression of cancers, including nasopharyngeal carcinoma (NPC). miR-539 was previously reported to be significantly downregulated in osteosarcoma. However, the potential role and mechanism of action of miR-539 in the initiation and progression of NPC remain largely unknown. Quantitative reverse transcription (RT)-PCR demonstrated that miR-539 was significantly downregulated in NPC tumour tissues compared with nontumour tissues. The cell viability, colony formation assay and tumourigenicity assays in nude mice showed that miR-539 could inhibit NPC cell growth in vitro and in vivo. The cyclin-dependent kinase 4 (CDK4) was verified as a miR-539 target gene using dual-luciferase reporter assays, quantitative RT-PCR and Western blotting and was involved in miR-539-regulated NPC cell growth. These results indicated that miR-539 plays an important role in the initiation and progression of NPC by targeting CDK4 and the miR-539/CDK4 pathway may contribute to the development of novel therapeutic strategies for NPC in the future. Copyright (C) 2015 John Wiley & Sons, Ltd.