Here, we present a novel plasma treatment regime—plasma fractionation, analogous to the concept of dose fractionation in radiotherapy, which could see the application in plasma-based cancer treatment. In plasma fractionation, a single acute dose of plasma is divided into multiple small dosages (fractionated dosages) and administered to the cells in vitro at 24-h intervals. We utilized a helium plasma jet and studied the effects of plasma fractionation in an immortalized keratinocyte line (HaCaT) and a squamous cell carcinoma line (A431). The effects were assessed over three cell seeding densities—8000, 3500, and 1000 cells/well. Our results show that at all seeding densities, plasma fractionation produced lower levels of cell death in both cell types compared to the same dose administered as a single plasma treatment. This highlights the potential of plasma fractionation as a potentially safer method to conduct plasma treatments in the future. We also show that A431 cells were more sensitive to a single acute plasma treatment than HaCaT cells, at cell densities that are subconfluent (1000 cells/well). A similar difference in sensitivity between HaCaT cells and A431 cells was not observed on exogenous treatment with hydrogen peroxide, pointing to the importance of other shorter lived plasma components.