Worldwide, breast cancer is the most frequently diagnosed life-threatening cancer in women and is the leading cause of cancer-related mortality among women. It is extremely rare but highly lethal in men. The deubiquitinating enzyme USP39 plays important roles in mRNA processing, and our previous data showed that high levels of USP39 are selectively present in different types of human breast tumor cells. The potential of USP39 as a therapeutic target for breast cancer was investigated. The expression levels of USP39 protein in 23 breast cancer specimens were quantified using an immunohistochemical assay and were found to have high levels in human breast cancer tissues when compared to these levels in normal breast tissues. In the breast cancer cell line MCF-7, USP39 expression was knocked down by a lentiviral short hairpin RNA (shRNA) delivery system. The RNA interference (RNAi)-mediated downregulation of USP39 expression markedly reduced the proliferative and colony forming ability of MCF-7 cells. In addition, the inhibition of USP39 induced G0/G1-phase arrest and apoptosis of the cells. These results suggest that USP39 may act as an oncogenic factor in breast cancer and could be a potential molecular target for breast cancer gene therapy.