Increasing evidence indicates that the dysregulation of miRNAs that act as tumor suppressors or oncogenes is involved in tumorigenesis. However, the role of miR-539 in hepatocellular carcinoma (HCC) has not been well investigated. Quantitative RT-PCR (qRT-PCR), proliferation assay, colony formation assay, migration and invasion assays, western blotting, and xenograft tumor growth models were performed to assess the expression levels and functions of miR-539 in HCC. Luciferase reporter assays, qRT-PCR, western blotting, and immunohistochemistry were used to identify and verify the targets of miR-539. miR-539 was significantly downregulated in HCC cell lines and tissue samples. Ectopic expression of miR-539 inhibited cell viability, proliferation, migration, and invasion in vitro and suppressed xenograft tumor growth in vivo. Fascin homologue 1 (FSCN1) was verified as a direct target of miR-539, and overexpression of FSCN1 promoted HCC cell migration and invasion. miR-539 acts as a novel tumor suppressor in the development and progression of HCC by targeting FSCN1, providing new insight into the mechanisms of HCC carcinogenesis and suggesting that miR-539 may be a therapeutic target.