Our study sought to clarify the effects of microRNA‐139‐5p (miR‐139‐5p) in the tumorigenesis and progression of oral squamous cell carcinoma (OSCC) by regulating HOXA9. MiR‐139‐5p and HOXA9 expression in OSCC tissues, tumour adjacent tissues, OSCC cells and normal cells were tested by qRT‐PCR. SAS and CAL‐27 cell lines were selected in among four OSCC cell lines and then transfected with miR‐139‐5p mimics, pEGFP‐HOXA9 and cotransfected with miR‐139‐5p mimics + pEGFP‐HOXA9. We used MTT, colony formation, transwell and wound healing assays to analyse cell viability, proliferation, invasion and migration. The target relationship between miR‐139‐5p and HOXA9 was verified by luciferase reporter assay and Western blot, respectively. MiR‐139‐5p was down‐regulated, whereas HOXA9 was up‐regulated in OSCC tissues and cells. The proliferation, invasion and migration ability of SAS and CAL‐27 cells in miR‐139‐5p mimics group were significantly weaker than those in the control group and the miR‐NC group (P < 0.01). MiR‐139‐5p can negatively regulate HOXA9. The proliferation, invasion and migration of SAS and CAL‐27 cells in the miR‐139‐5p mimics + pEGFP‐HOXA9 group were not significantly different from those in the blank control and negative control groups (P > 0.05). Our results indicated that miR‐139‐5p could directly inhibit HOXA9, which might be a potential mechanism in inhibiting the proliferation, invasiveness and migration of OSCC cells.