We present a novel active mixing method in a microfluidic chip, where the controlled stirring of magnetic particles is used to achieve an effective mixing of fluids. To perform mixing, the ferromagnetic particles were embedded and manipulated under the influence of a rotating magnetic field. By aligning the magnetic beads along the magnetic field lines, rod-like structures are formed, functioning as small stir bars. Under higher flow conditions the particles did not form the typical rod structure but rather formed aggregates, which were even more beneficial for mixing. Our system reached a 96% mixing efficiency in a relatively short distance (800 microm) at a flow rate of 1.2-4.8 mm/s. These results demonstrate that our mixing method is useful for microfluidic devices with low aspect ratios and molecules with large molecular weights.