Chondrosarcomas rank as the third most common type of bone tumors. In the present study, we demonstrated that expression of the apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3B (APOBEC3B) was higher in cancer tissues when compared to that in normal tissues. In order to further investigate the effects of APOBEC3B expression, we knocked down APOBEC3B expression in chondrosarcoma cells. We found that the percentage of apoptotic cells was higher in the APOBEC3B-knockdown cells than the percentage in the untransfected cells. Furthermore, we found that the reduced antitumor activity of RUNX3 was caused by APOBEC3B. Finally, we demonstrated that caspase-3, -8 and -9 activity was significantly increased in the RUNX3-expressing cells with APOBEC3B knockdown. In summary, our results indicate that APOBEC3B knockdown may be a useful therapy to enhance apoptosis in chondrosarcoma.