A low-cost electrochemical biosensor, assisted by a new type of functional magnetic nanoparticles (NPs), has been developed to detect eosinophil cationic protein (ECP), a known biomarker of asthma, in cell culture. The heparin-modified magnetic NPs were mixed with a sample solution containing ECP. After ECP had been captured by the NPs, a magnetic field was applied behind a graphite-based screen-printed electrode. The functional magnetic NPs were attracted to the electrode, raising the ECP concentration near its surface. Because of the use of the functional magnetic NPs, the difference in the signal was amplified when applying larger sample volumes for detection, thereby enhancing the sensitivity of the biosensor. This approach provided a linear range for the analysis of the logarithm of the ECP concentration from 1 to 1000 nM, with a coefficient of determination 0.992; the limit of detection was 0.30 nM. The fabricated biosensor displayed good recovery in a cell culture medium incubated with the Beas–2 B cell line. The ability to detect the concentration of ECP in a cell culture at any time point should be useful for explaining contradictory findings regarding the relationship between the initial ECP concentration and the cell line.