Growing evidence indicates that some abnormally expressed microRNAs (miRNAs) influence tumorigenesis and progression. Previous studies reported that miR-20a is among the frequently altered miRNAs in human hepatocellular carcinoma (HCC), but its expression pattern and role in HCC remain controversial. In the present study, we demonstrated that miR-20a-5p exhibited aberrant expression in HCC tissues compared with paired non-tumor tissues: 52% of the tumor samples showed a greater increase. Overexpression of miR-20a contributed to HCC cell proliferation and migration in vitro, and treatment with anti-miR20a-5p caused the opposite effects. Further studies revealed RUNX3, an important tumor-suppressor, as a direct target of miR-20a-5p. We observed that the level of RUNX3 was sharply reduced in both mRNA and protein in HCC tissues compared with paired non-tumor tissues. Collectively, our results support the viewpoint that miR-20-5p has an oncogenic property, miR-20a overexpression contributed to HCC cell proliferation and migration through reducing the translation of RUNX3. The data provide a new mechanism of miR-20a regulating RUNX3 in HCC.