Extracellular vesicles (EVs) are promising biomarkers for diagnosing complex diseases such as cancer and neurodegenerative disorders. Yet, their clinical application is hindered by challenges in isolating cancer-derived EVs efficiently due to their broad size distribution in biological samples. This study introduces a microfluidic device fabricated using off-stoichiometry thiol-ene and cyclic olefin copolymer, addressing the absorption limitations of polydimethylsiloxane (PDMS). The device streamlines a standard laboratory assay into a semi-automated microfluidic chip, integrating sample mixing and magnetic particle separation. Using the microfluidic device, the binding kinetics between EVs and anti-CD9 nanobodies were measured for the first time. Based on the binding kinetics, already after 10 min the EV capture was saturated and comparable to standard laboratory assays, offering a faster alternative to antibody-based immunomagnetic protocols. Furthermore, this study reveals the binding kinetics of EVs to anti-CD9 nanobodies for the first time. Our findings demonstrate the potential of the microfluidic device to enhance clinical diagnostics by offering speed and reducing manual labor without compromising accuracy.