Bladder cancer (BC) is a disease that requires lifelong surveillance due to its high recurrence rate. An efficient method for the non-invasive rapid monitoring of patient prognosis and downstream phenotype characterization is warranted. Here, we develop an integrated procedure to detect aggressive mesenchymal exfoliated bladder cancer cells (EBCCs) from patients in a label-free manner. Using a combination of filtration and inertial focusing principles, the procedure allowed the focusing of EBCCs in a single stream-line for high-throughput separation from other urine components such as large squamous cells and blood cells using a microfluidic sorting device. Characterization of enriched cells can be completed within hours, suggesting a potential utility for real-time detection. We also demonstrate high efficiency of cancer cell recovery (93.3 ± 4.8%) and specific retrieval of various epithelial to mesenchymal transition (EMT) phenotype cell fractions from respective outlets of the microfluidic device. EMT is closely associated with metastasis, drug resistance and tumor-initiating potential. This procedure is validated with clinical samples, and further demonstrate the efficacy of bladder wash procedure to reduce EBCCs counts over time. Overall, the uniqueness of a rapid and non-invasive method permitting the separation of different EMT phenotypes shows high potential for clinical utility. We expect this approach will better facilitate the routine screening procedure in BC and greatly enhance personalized treatment.