Magnetic microspheres (MMS) are useful tools for a variety of medical and pharmaceutical applications. Typically, commercially manufactured MMS exhibit broad size distributions. This polydispersity is problematic for many applications. Since the direct synthesis of monodisperse MMS is often fraught with technical challenges, there is considerable interest in and need associated with the development of techniques for size-dependent fractionation of MMS. In this study we demonstrated continuous size-dependent fractionation of sub-micron scale particles driven by secondary (Dean effect) flows in curved microfluidic channels. Our goal was to demonstrate that such techniques can be applied to MMS containing superparamagnetic nanoparticles. To achieve this goal, we developed and tested a microfluidic chip for continuous MMS fractionation. Our data address two key areas. First, the densities of MMS are typically in the range 1.5–2.5 g/cm3, and thus they tend be non-neutrally buoyant. Our data demonstrate that efficient size-dependent fractionation of MMS entrained in water (density 1 g/cm3) is possible and is not significantly influenced by the density mismatch. In this context we show that a mixture comprising two different monodisperse MMS components can be separated into its constituent parts with 100% and 88% success for the larger and smaller particles, respectively. Similarly, we show that a suspension of polydisperse MMS can be separated into streams containing particles with different mean diameters. Second, our data demonstrate that efficient size-dependent fractionation of MMS is not impeded by magnetic interactions between particles, even under application of homogeneous magnetic fields as large as 35 kA/m. The chip is thus suitable for the separation of different particle fractions in a continuous process and the size fractions can be chosen simply by adjusting the flow velocity of the carrier fluid. These facts open the door to size dependent fractionation of MMS.