In this study, a new magnetic field flow fractionation (FFF) system was designed and modeled by using finite element simulations. Other than current magnetic FFF systems, which use static magnetic fields, our system uses cyclical magnetic fields. Results of the simulations show that our cyclical magnetic FFF system can be used effectively for the separation of magnetic nanoparticles. Cyclical magnetic FFF system is composed of a microfluidic channel (length = 5 cm, height = 30 μm) and 2 coils. Square wave currents of 1 Hz (with 90 deg of phase difference) were applied to the coils. By using Comsol Multiphysics 3.5a, magnetic field profile and corresponding magnetic force exerted on the magnetite nanoparticles were calculated. The magnetic force data were exported from Comsol to Matlab. In Matlab, a parabolic flow profile with maximum flow speed of 0.4 mL/h was defined. Particle trajectories were obtained by the calculation of the particle speeds resulted from both magnetic and hydrodynamic forces. Particle trajectories of the particles with sizes ranging from 10 to 50 nm were simulated and elution times of the particles were calculated. Results show that there is a significant difference between the elution times of the particles so that baseline separation of the particles can be obtained. In this work, it is shown that by the application of cyclical magnetic fields, the separation of magnetic nanoparticles can be done efficiently.