Abstract—Separation techniques in microfluidic devices using magnetic fields are well-known in biomedical applications in disease diagnosis like cancer, drug delivery, and hyperthermia. In this work, a microfluidic system is investigated. Here magnetic nanoparticles are separated from their medium using magnetic force. The whole microfluidic device for separation of functionalized magnetic beads is composed of a fluidic part and a magnetic part. The diameters of applied nanoparticles are 90 nm, 200 nm and 750 nm. In this method, magnetic nanoparticles are injected into a microchannel, the permanent magnet is located under the channel and the magnetic field which is produced by permanent magnet is applied to the nanoparticles, so the magnetic nanoparticles are integrated above the permamnet magnet. Trajectory of particles, velocity, and the location in which magnetic nanoparticles are captured are obtained.