This paper proposes the use of a 3D extrusion printer to fabricate artificial magnetic cilium. The cilia are fabricated using polydimethylsiloxane (PDMS) doped with iron particles so that they remain slender and flexible. They can be driven by a magnetic field to closely mimic the behaviour of biological cilia. Doping iron particles to the polymers has already been done; however, to the best of our knowledge, printing such active and soft magnetic structures has not. The existing methods for manufacturing magnetic polymeric structures are complex and difficult to use for the fabrication of micro-sized high-aspect-ratio cilia. The 3D printing technique we propose here is simple and inexpensive compared to previously suggested fabrication methods. In this study, free-standing magnetic PDMS cilia were fabricated in different sizes up to 5 mm in length and 1 mm in width. The stress-strain curves of the PDMS cilia were experimentally obtained to quantify the effect of the concentration of the iron particles on the modulus of elasticity of the cilia. The higher the iron concentration, the higher the modulus of elasticity. We have quantified the characteristics of the cilia made of 40% w/w iron particles in PDMS. A single cilium (5×1×0.0035 mm) can output up to 27 μN blocking force under a magnetic field of 160 mT. These cilia can be used as a mixer in lap-on-chip applications and as the anchoring and propulsion legs of endoscopic capsule robots operating within the gastrointestinal tract of humans. Analytical expressions estimating the blocking force are established and compared with the experimental results.