Nasopharyngeal carcinoma (NPC) is a major cause of cancer deaths. Concurrent administration of radiation and chemotherapy is the treatment of choice for advanced NPC. Previously, we showed that apogossypolone (ApoG2) induced apoptosis by blocking the binding of Bcl-2 to Bax, arresting the cell cycle in the S phase, in turn inhibiting proliferation of NPC cells both in vitro and in vivo. In the present study, we showed that ApoG2 inhibited the proliferation of NPC cells in a dose-dependent manner. We treated CNE1, CNE2 and SUNE1 cells with ApoG2 for 72 h, and calculated the IC50 values as 2.84, 5.64 and 2.18 µM, respectively. Normal NP69 cell proliferation was not significantly inhibited. ApoG2 treatment induced significant autophagy, demonstrated by an increase in LC3-II protein expression, reduced protein p62 expression, and accumulation of punctuate GFP-LC3 in the cytoplasm of CNE1 or CNE2 cells. Sh-Atg5 attenuated the autophagy induced by ApoG2, indicating that Atg5 was required for ApoG2-induced autophagy. In addition, ApoG2 treatment blocked the binding of Bcl-2 to Beclin 1 protein, releasing pro-autophagic Beclin 1, which in turn triggered the autophagic cascade. Colony formation assays indicated that ApoG2 enhanced radiosensitization of CNE2 cells. In the ApoG2-plus-radiation combination group, more ring-shaped structures were evident in CNE1 and CNE2 cultures. LC3-II expression was enhanced and that of p62 reduced, compared to the ApoG2-only, radiation-only and control groups. ApoG2 enhanced the radiosensitivity of CNE2 xenografts in nude mice as measured by (C-T)/C ratios (as percentages); the values for the ApoG2 and radiation groups were 46.89% and 19.34%, respectively. The ApoG2-plus-radiation group exhibited greater antitumor activity (the inhibitory rate was 61.64%). Immunohistological staining showed that LC3-II expression became gradually upregulated in the ApoG2-plus-radiation group. Together, the results suggest that ApoG2 inhibits the binding of Bcl-2 to Beclin 1, inducing autophagy and radio-sensitizing NPC cells both in vitro and in vivo.