Early cancer detection greatly enhances the prognosis and allows for higher treatment success. Cancer metastasis, which occurs in later stages, is believed to cause more than 90% of cancer-related deaths 1. In earlier cancer stages, circulating tumor cells (CTCs) may be detected in the blood of cancer patients, which can correlate with patient survival rate. Accurate, non-invasive separation of these cells allows for early detection of cancer and aids in increasing therapeutic efficacy 2. This work provides an integrated on-chip quantitative cell sorting platform that separates and counts magnetically labeled cells through a microfluidic channel. First, an immunomagnetic assay is utilized to label CTCs with highly selective magnetic nanoparticles. Then, magnetically labeled cells are separated and guided through the microfluidic channel by electromagnetics and ferromagnetic strips 3. After cell separation, magnetically labeled biomarkers are detected by the magnetic tunnel junction (MTJ) sensor that measures stray fields surrounding the labeled CTCs, generating an electrical signal for each passing particle. Additionally, biomarkers with different sizes, such as CTCs and protein-based cancer biomarkers, can be detected and quantified as they move through the microfluidic channel at different speeds, yielding distinct peaks at the MTJ output 3. This work demonstrates a highly selective platform that actively sorts magnetically labeled biomarkers by combining magnetophoresis-based cell sorting and MTJ-based flow cytometry allowing for highly sensitive quantitative on-chip cell sorting.