HOXB5, a member of the HOX gene family, is a developmental gene which encodes homeoproteins and is known to be a crucial player in development of enteric nervous systems. Recently, HOXB5 was reported to be associated with cancer progression. However, the specific effect of HOXB5 in hepatocellular carcinoma (HCC) remains unclear. In this study, we demonstrated the important role of HOXB5 in HCC. We showed that HOXB5 was up-regulated in HCC tissues and cell lines. Furthermore, down-regulation of HOXB5 inhibited TGF-β-induced HCC cell migration and invasion in vitro and suppressed tumor metastasis in vivo. We also found that the PI3K/Akt pathway partly accounted for the mechanisms underlying the inhibitory effect of HOXB5 down-regulation on TGF-β-induced HCC progression. Taken together, these findings demonstrated that down-regulation of HOXB5 inhibits TGF-β-induced migration and invasion in HCC cells via inactivation of the PI3K/Akt pathway. Thus, HOXB5 may be a novel therapeutic target for HCC treatment.