Breast cancer is one of the most common malignant diseases among women worldwide, and the existence of breast cancer stem cells is closely associated with poor outcomes. Herein, we report an electrochemical phenotyping method to characterize the stemlike phenotype in breast cancer, offering a low-cost but robust choice other than the highly expensive and experience-dependent flow cytometry. Specially, after immune-magnetic beads-assisted enrichment, an in situ programmable DNA circuit is designed using capture probes to bring in the toeholds for DNA assembly and effector probes to accelerate the removal of background signals. The electrochemical phenotyping method could sensitively determine breast cancer stem cells in a wide linear range and exhibit desirable accuracy and reliability. The method can not only monitor the phenotypic transition of breast cancer cells and the drug-reversed effect but also determinate stemlike phenotype in the mice bearing breast cancer xenograft tumor. Overall, the electrochemical phenotyping method may provide promising technical support for precise management of breast tumors.