Ensembles of magnetic particles are known to align and aggregate into multi-particle clusters in an applied magnetic field, and the physical laws governing these processes are well-described in literature. However, it has been elusive how to achieve the opposite process, i.e. the disaggregation of particle clusters in a magnetic field. We report a novel method to disaggregate clusters of superparamagnetic microparticles using time-dependent magnetic fields. The disaggregating field is designed to generate repulsive dipole-dipole forces between the particles and to stabilize the disaggregated particles on a physical surface. We demonstrate the disaggregation of large clusters of several tens of particles, within about of one minute, using fields generated by a multipole electromagnet. After the disaggregation process the particles are uniformly distributed over the surface and ready for further lab-on-chip processing. Our results represent a novel methodology to disaggregate magnetic particle clusters and thereby improve the effectiveness and reproducibility of biological assays based on magnetic microparticles.