This study presents a new suction-type microfluidic system capable of rapid measurement of alpha-fetoprotein (AFP) by utilizing magnetic bead-based technologies. Two modules, including a suction-type incubator for the magnetic beads to capture AFP and acridinium ester (AE)-labeled anti-AFP antibodies and a microfluidic control module for sample transportation, were integrated into this microfluidic system. With the incorporation of AFP-specific aptamer-conjugated magnetic beads, the target AFP could be recognized and attracted onto the surface of the magnetic beads from the clinical sample. The entire process including two-step incubation and purification process could be automatically performed within 25 min, which is only about 20% of the time required when using a benchtop machine (for about 130 min). Besides, the total sample and reagent volume consumed is only 105 μL, which is significantly less than that required in a large system (410 μL). More importantly, experimental results showed that clinical human serum samples can also be accurately analyzed. The microfluidic system may be promising for point-of-care applications for AFP detection in the future.