This paper presents a mathematical model of the detection of the magnetic nanoparticles (MNPs) flowing into a microchannel. To validate the model, the experimental measurements were performed using a ferrofluid and a giant magneto impedance microwire made up of CoFeSiBNb alloy as a sensor. The good agreement between theory and measurement implies the possibility of using the numerical simulation to analyze the system performance for the MNPs detection. In addition, a model calculation was performed, which evaluates the optimal signal-to-noise ratio of the detection system as a function of its main parameters and according to the magnetic induction induced by the MNPs.