Brucea javanica fruit has been used to treat amebic dysentery, malaria and various parasites and it has been applied as an anti-cancer agent in Traditional Chinese Medicine. Brucein D (BD) is a naturally occurring compound extracted from Brucea javanica fruit which shows anti-cancer activity against pancreatic cancer. Here, we further demonstrated that BD inhibited hepatocellular carcinoma (HCC) cell growth in vitro and tumor growth in vivo that were attributed to the induction of cell apoptosis. BD did not exert growth inhibition on non-tumorigenic human hepatocytes. MTT assay was used to measure cell viability. Annexin V and TUNEL assay were applied to identify apoptotic cells in cell suspension and in tissue section respectively. Downstream micro-RNA (miRNA) targets of BD were screened out by miRNA array. miRNAs and their target proteins were identified by bioinformatics analysis and luciferase reporter assay. 39 miRNAs regulated by BD in HCC were identified. miR-95 was found to be a potential drug target of BD. We further identified CUG triplet repeat RNA-binding protein 2 (CUGBP2) as the downstream target of miR-95. Our data suggested that BD exerted its anti-cancer activity against HCC through modulation of miR-95 expression.