Hepatocellular carcinoma (HCC) is the fifth most common cancer in the world. However, little is known regarding the molecular mechanism of HCC development and progression and effective therapeutic methods. Recently, the granulin-epithelin precursor (GEP) was reported as a novel growth factor that can control HCC cell proliferation. Using the CAPSID program, we designed three small interfering RNAs (siRNAs) targeting the GEP gene (GEP-siRNA1, 2 and 3) and examined their tumor regression and suppression effects on cell proliferation. GEP-siRNA1 exhibited the strongest anti-proliferative effect among the GEP-siRNAs, in a time-dependent manner. To increase the biostability of the siRNA, we also constructed a short hairpin RNA (shRNA) using an H1/TO promoter with the same sequence of GEP-siRNA1 (GEP-shRNA). GEP-shRNA decreased the expression levels of GEP and tumor cell growth via cell cycle arrest at the G2/M stage and down-regulation of the cell proliferation proteins cyclin D1 and α-tubulin. Furthermore, GEP-shRNA inhibited tumor growth significantly after intratumoral injection into tumor-bearing Balb/C nude mice. Taken together, these results represent the first therapeutic application of RNA interference to GEP, which is a promising target molecule for HCC treatment, as an approach for the suppression of HCC cell proliferation.