Cold atmospheric plasma (CAP) was shown to affect cells not only directly, but also indirectly by means of plasma pre-treated solution. This study investigated a new application of CAP generated in deionized (DI) water for the cancer therapy. In our experiments, the CAP solution was generated in DI water using helium as carrier gas. We report on the effects of this plasma solution in breast (MDA-MD-231) and gastric (NCI-N87) cancer cells. The results revealed that apoptosis efficiency was dependent on the plasma exposure time and on the levels of reactive oxygen and nitrogen species (ROS and RNS). The plasma solution that resulted from 30-minute treatment of DI water had the most significant effect in the rate of apoptosis.