In this paper, we introduce a method to exploit ultra-high dielectrophoresis (UHF-DEP) with a microfluidic radio frequency device able to sort biological cells by deflecting the trajectory of the targeted population in a continuous flow. This study highlights the capability of a high frequency lab-on-chip implemented UHF-DEP cytometer to isolate cancer stem cells (CSCs). Actually, CSCs sorting by an efficient, fast and low-cost method remains an issue. Above 20 MHz, the intracellular dielectric properties of cells determine the dielectrophoretic behavior of cells and is then very sensitive to the cell cytoplasm content. The proposed cell sorting principle exploits the combination of the fluidic drag and the repulsive dielectrophoretic forces in order to isolate CSCs hidden within differentiated cancer cells. We previously demonstrated the UHF-DEP behavior of cells, as a new type of electromagnetic biomarkers to discriminate cancer stem cells among a tumor population from colorectal cancer cell line.