Superparamagnetic nanoparticles are attracting significant attention. Therefore, being explored in microsystems for a wide range of applications. Typical examples include lab-on-a-chip and microfluidics for synthesis, detection, separation, and transportation of different bioanalytes, such as biomolecules, cells, and viruses to develop portable, sensitive, and cost-effective biosensing systems. Particularly, microfluidic systems incorporated with magnetic nanoparticles and, in combination with magnetoresistive sensors, shift diagnostic and analytical methods to a microscale level. In this context, nanotechnology enables the miniaturization and integration of a variety of analytical functions in a single chip for manipulation, detection, and recognition of bioanalytes reliably and flexibly. In consideration of the above, recent development and benefits are elaborated herein to discuss the role of magnetic nanoparticles inside the microchannels to design highly efficient disposable point-of-care applications from transportation to the detection of bioanalytes.