Rapid detection of a biological agent is essential to anticipate a threat to the protection of biodiversity and ecosystems. Our goal is to miniaturize a magnetic pathogen detection system in order to fabricate an efficient and portable system. The detection device is based on flat, multilayer coils associated with microfluidic structures to detect magnetic nanoparticles linked to pathogen agents. One type of immunological diagnosis is based on the measurement of the magnetic sensitivity of magnetic nanoparticles (MNPs), which are markers connected to pathogens. This method of analysis involves the coupling of antibodies or antigen proteins with MNPs. Among the available magnetic techniques, the frequency mixing method has a definite advantage by making it possible to quantify MNPs. An external magnetic field composed of a low- and a high-frequency field is applied to the sample reservoir. Then, the response signal is measured and analyzed. In this paper, magnetic microcoils are implemented on a multilayer Printed Circuit Board (PCB), and a microfluidics microstructure is designed in connection with the planar coils. Simulation software, COMSOL version 5.3, provides an analytical perspective to choose the number of turns in magnetic coils and to understand the effects of changing the shape and dimensions of the microfluidics microstructure.