Objective: To investigate the miR-96 expression in hepatocellular carcinoma (HCC) cells and its actions. Methods: The miR-96 expressions in different HCC cell lines (HepG2, 7721 and huh7) and normal hepatic L02 cells were measured by qRT-PCR. The HepG2 cells were transfected with scrambled miRNA sequence (negative control group), miR-96 mimics (miR-96 mimics group) and miR-96 inhibitors (miR-96 inhibitors group) respectively, and then, the cell migration and invasion abilities were examined by cell wound scratch assay and Transwell assay, and the expressions of PTPN9 mRNA and protein were determined by qRT-PCR and Western blot, respectively. Results: The miR-96 expressions were significantly higher in all studied HCC cell lines than that in normal hepatic L02 cells (all P<0.01). Compared with negative control group, the wound healing rate was significantly increased in miR-96 mimics group, and was significantly decreased in miR-96 inhibitors group (both P<0.05); the number of invading cells was significantly increased in miR-96 mimic group, and was significantly decreased in miR-96 inhibitors group (both P<0.05); both PTPN9 mRNA and protein expression levels were significantly down-regulated in miR-96 mimics group, and were significantly up-regulated in miR-96 inhibitors group (all P<0.05). Conclusion: MiR-96 expression is increased in HCC cells, which may promote the migration and invasion abilities of HCC cells by down-regulating PTPN9 expression.