Magnetic artificial cilia (MAC) are flexible hair-like micro-actuators inspired by biological cilia. When integrated in a microfluidic device and actuated by an external (electro-)magnet, MAC can generate fluid flows. Our MAC are made of a composite material of polydimethylsiloxane (PDMS) and magnetic microparticles (Carbonyl iron powder). In this paper, we demonstrate a fabrication process based on micro-moulding to manufacture MAC, in which we can vary the magnetic particle distribution within the cilia from (1) a random distribution, to (2) a linearly aligned distribution to (3) a concentrated distribution in the tips of the cilia. Magnetization measurements show that the aligned distribution leads to a substantial increase of magnetic susceptibility, which dramatically enhances their response to an applied magnetic field. When integrated in a microfluidic channel, the improved MAC can induce versatile flows, for example (i) circulatory fluid flows with flow speeds up to 250 μm/s which is substantially above the performance of most of the previously developed artificial cilia, (ii) direction-reversible flows, (iii) oscillating flows, and (iv) pulsatile flows, by changing the magnetic actuation mode. Compared to other pumping methods, this on-chip/in-situ micro-pump requires no tubing or electric connections, reducing the usage of reagents by minimizing “dead volumes” avoiding undesirable electrical effects, and accommodating a wide range of different fluids. These results demonstrate that our MAC can be used as versatile integrated micropump in microfluidic devices, with great potential for future lab-on-a-chip applications.