Magnetic nanoparticles are commonly used in numerous applications such as magnetic resonance imaging (MRI), local hyperthermia treatment, magnetic separation, information storage, and medical diagnostics using magnetic immunoassays. The latter field has become increasingly popular in the last years because of the favorable properties of magnetic particles. In fact, the particles can be used both for magnetic actuation as well as for magnetic detection of biomolecules. In the case of immunoassays, the magnetic beads are bound to the biological target substance using the highly specific antibody-antigen interaction. The most common assay format is the sandwich immunoassay in which the analyte is captured by an immobilized primary antibody and the streptavidin-coated magnetic particles are bound to the analyte by a biotinylated secondary antibody. This article reports the conception and realization of a magnetic detection system that encompasses a microfluidic structure along with multilayer designed set of planar coils in a printed circuit board (PCB). The challenge is to measure the magnetic marker particles with high accuracy and high selectivity using a small quantity of biological sample. The magnetic frequency mixing technique is very well suited for this purpose of immunoquantification. For this concept, analytical calculations along with Comsol Multiphysics simulations have been achieved to optimize the dimensions of the coils and the microfluidic reservoir.