The present study reports the design and synthesis of new 1,3-diphenylquinoxaline-6-carboxamide derivatives 5a-l as promising anticancer agents. Cytotoxicity of these compounds was evaluated against cancer cell lines MDA-MB-231, MCF-7, and HeLa and the obtained data were compared to Etoposid that is a known anti-cancer drug. The best compound against the latter cell lines was compound 5c. This compound acted better than Etoposide against all three cell lines MDA-MB-231, MCF-7, and HeLa. Therefore, additional in vitro and in silico studies were performed on compound 5c. Flow cytometry studies on compound 5c showed that this compound clearly induces apoptosis. In silico study in the binding site of Etoposide in DNA topoisomerase IIα showed that compound 5c interacts with this enzyme with a binding energy comparable to Etoposide.