microRNAs (miRNAs) are short single-strand non-coding RNAs that regulate various cell processes at the post-transcriptional levels. Mounting evidences suggested that dysregulation of miRNA is associated with cancer progression and development. The aberrant expression of miR-339-5p has been found in some types of cancers, however, the association of miR-339-5p expression and hepatocellular carcinoma (HCC) is still unclear. Here, we measured the expression of miR-339-5p in HCC tissues and explored its clinicopathological and prognostic significance. The result showed that miR-339-5p expression level was significantly lower in HCC tissues compared with non-cancerous liver tissues. Moreover, patients with lower miR-339-5p expression level are associated with a poorer overall survival. Multivariate Cox regression analysis showed that the expression of miR-339-5p was an independent prognostic factor for HCC patients. In addition, we found that over-expression of miR-339-5p can inhibit HCC cell invasion. In conclusion, our results indicated that miR-339-5p may serve as a tumor suppressor and play important role in inhibiting tumor invasion. Our work implicates that miR-339-5p may serve as a prognostic marker and molecular therapeutic target in HCC.