Microfluidic chip and giant magnetoimpedance (GMI)-related technology has developed quickly over the past decades in the field of biological detection. In this work, we designed and fabricated a GMI-based microfluidic system for screening of multiplex gastric cancer biomarkers. The microfluidic chip and GMI sensor were prepared by micro-electromechanical systems (MEMS) technology. This system can analyse 8 gastric cancer protein biomarkers simultaneously in less than 25 mins and offer more stable detection signal than conventional enzymological or fluorescent methods. The microfluidic chip was then tested in 150 clinical specimens and compared with enzyme-linked immunosorbent assay (ELISA) method. The results indicated no significant difference and excellent agreement. In short, the prototype of GMI-based microfluidic system has been developed successfully and showed promising potentials for parallel screening of cancer biomarkers.