Prostate cancer is the second cause of cancer-related deaths in men worldwide, and new agents for curing the disease are still needed. In this study, we theoretically and experimentally demonstrated that valeric acid (VA) was a HDAC inhibitor, and anti-cancer efficacy of VA in prostate cancer cells was also observed using either 2D or 3D culture systems. VA was cytotoxic for prostate cancer cells but low toxic to normal cells. VA significantly inhibited E2F1/E2F3 expression but increased CASP3 activity. In vivo mouse models further showed its anti-cancer activity and potential property of chemosensitizer with promoting apoptosis. The findings suggest that VA acts as a HDAC3 inhibitor with anti-cancer effect on prostate cancer by regulating E2F1/E2F3/CASP3 axis.