In this paper, we report a new micromixer based on a flexible artificial cilium activated by an external magnetic field. The cilium is fabricated from Polydimethylsiloxane doped with Fe microparticles. The fabrication method is based on the standard sacrificial layer technology. The cilium was built on a glass slide, and then was bonded on the top of the micro-mixer chamber in a microfluidic chip. This fabrication process for the miniaturized active mixers is simple and cost effective. An electromagnetic system was used to drive the cilium and induce strong convective flows of the fluid in the chamber. In the presence of an alternating magnetic field, the cilium applied a corresponding alternating force on the surrounding fluids. The performance of the electromagnetically activated cilium was quantified and optimized in order to obtain maximum mixing performance. In addition, the mixing performance of the cilium in a circular micro-chamber was compared with pure diffusion. Up to 80% of a 60 ul liquid in the chamber can be fully mixed after 2 min using a cilium mixer under a magnetic flux density of 22 mT in contrast to the 20 min which were needed to obtain the same mixing percentage under pure diffusion. Furthermore, for a mixing degree of 80%, the mixing speed for the cilia micromixer proposed in this study was 9 times faster than that of the diffusion-based micro-mixers reported in the literature.