Bee venom (BV) secreted from the venom gland of the honey bee contains several biological active compounds. BV has been widely used as a traditional medicine for treating human disease, including cancer. In this study, we have shown the molecular mechanism underlying the therapeutic effect of BV on cancer. Treatment with BV reduced the proliferation of cervical cancer cells in a dose and time dependent manner. Interestingly, the killing effect of BV was specific to HPV-positive cervical cancer cell lines, such as Caski and HeLa cells, and not to HPV-negative cervical cancer cells (C33A). BV reduced the expression of HPV E6 and E7 at RNA and protein levels, leading to an increase in the expression of p53 and Rb in Caski and HeLa cells. Further, BV decreased the levels of cell cycle proteins such as cyclin A and B and increased the levels of cell cycle inhibitors such as p21 and p27. BV significantly induced apoptosis and inhibited wound healing and migration of cervical cancer cells. It also upregulated the expression of pro-apoptotic BAX and downregulated the expression of anti-apoptotic Bcl-2 and Bcl-XL. Cleavage of caspase-3, caspase-9, and PARP were also induced by BV treatment, while the phosphorylation of mitogenic signaling-related proteins such as AKT, JNK, p38, and ERK were downregulated. Our results indicate that BV has a therapeutic selectivity for HPV-positive malignant cells, therefore further clinical studies are needed to assess its clinical application.