There is great interest in highly sensitive separation methods capable of quickly isolating a particular cell type within a single manipulation step prior to their analysis. We present a cell sorting device based on the opposition of dielectrophoretic forces that discriminates between cell types according to their dielectric properties, such as the membrane permittivity and the cytoplasm conductivity. The forces are generated by an array of electrodes located in both sidewalls of a main flow channel. Cells with different dielectric responses perceive different force magnitudes and are, therefore, continuously focused to different equilibrium positions in the flow channel, thus avoiding the need of a specific cell labeling as discriminating factor. We relate the cells’ dielectric response to their output position in the downstream channel. Using this microfluidic platform that integrates a method of continuous-flow cell separation based on multiple frequency dielectrophoresis, we succeeded in sorting viable from nonviable yeast with nearly 100% purity. The method also allowed to increase the infection rate of a cell culture up to 50% of parasitemia percentage, which facilitates the study of the parasite cycle. Finally, we prove the versatility of our device by synchronizing a yeast cell culture at a particular phase of the cell cycle avoiding the use of metabolic agents interfering with the cells’ physiology.