This paper presents a custom, low-cost electronic system specifically designed for rapid and quantitative detection of the malaria parasite in a blood sample. The system exploits the paramagnetic properties of malaria-infected red blood cells (iRBCs) for their magnetophoretic capture on the surface of a silicon chip. A lattice of nickel magnetic micro-concentrators embedded in a silicon substrate concentrates the iRBCs above coplanar gold microelectrodes separated by 3 μm for their detection through an impedance measurement. The sensor is designed for a differential operation to remove the large contribution given by the blood sample. The electronic readout automatically balances the sensor before each experiment and reaches a resolution of 15 ppm in the impedance measurement at 1 MHz allowing a limit of detection of 40 parasite/μl with a capture time of 10 minutes. For better reliability of the results, four sensors are acquired during the same experiment. We demonstrate that the realized platform can also detect a single infected cell in real experimental conditions, measuring human blood infected by Plasmodium falciparum malaria specie.