In this paper, we studied the functional effects of cold atmospheric plasma (CAP) on the esophageal cancer cell line (KYSE-30) by direct and indirect treatment and fibroblast cell lines as normal cells. KYSE-30 cells were treated with CAP at different time points of 60, 90, 120 and, 240 s for direct exposure and 90, 180, 240 and, 360 s for indirect exposure. Cell viability was studied by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and apoptosis induction in the treated cells was measured by Annexin-V/PI using flow cytometry. The expression of apoptotic related genes (BAX/BCL-2) was analyzed by real-time polymerase chain reaction. Moreover, the genotoxicity was analyzed by comet assay. Cell viability results showed that direct CAP treatment has a markedly cytotoxic impact on the reduction of KYSE-30 cells at 60 s (p = 0.000), while indirect exposure was less impactful (p > 0.05). The results of the Annexin-V/PI staining confirmed this analysis. Subsequently, the genotoxicity study of the direct CAP treatment demonstrated a longer tail-DNA length and caused increase in DNA damage in the cells (p 0.05). Treatment with direct CAP showed genotoxicity in cancer cells. Collectively, our results pave a deeper understanding of CAP functions and the way for further investigations in the field of esophageal cancer treatment.