Melatonin exhibits oncostatic activity in several cancers but does not lead to cytotoxicity in estrogen receptor (ER)-negative non-small cell lung cancers (NSCLCs). In an effort to overcome the melatonin resistance of these cancers, we investigated whether cell cycle and apoptosis regulator 2 (CCAR2) depletion would promote apoptosis following genotoxic stress in melatonin-resistant cancer cells. Ordinarily, the NSCLC cell lines A549 and A427 did not undergo cell death following melatonin treatment for short period. These cell lines were irradiated with UV, a source of genotoxic damage, to trigger apoptotic signaling. Treatment with melatonin prior to irradiation did not produce any significant change in apoptosis. By contrast, in CCAR2-deficient cells, melatonin treatment increased apoptosis induced by genotoxic stress; this effect was dependent on the dose of melatonin. The increase in apoptosis in CCAR2-deficient cells was not dependent on SIRT1. The results indicate that CCAR2 is critical for maintaining cell survival in the presence of melatonin under genotoxic stress. Furthermore, CCAR2 is overexpressed in NSCLC; therefore, melatonin could be used as a potential supplement to classical anticancer drugs in therapies against CCAR2-deficient cancers.