There is a critical need for novel approaches to translate cell therapy and regenerative medicine to clinical practice. Magnetic cell targeting with site-specificity has started to open avenues in these fields as a potential therapeutic platform. Magnetic targeting is gaining popularity in the field of biomedicine due to its ability to concentrate and retain at a target site while minimizing deleterious effects at off-target sites. It is regarded as a relatively straightforward and safe approach for a wide range of therapeutic applications. This review discusses the latest advancements and approaches in magnetic cell targeting using endocytosed and antibody-conjugated magnetic nanoparticles as well as in vivo tracking using MRI. The most common form of magnetic particles is superparamagnetic iron-oxide nanoparticles (SPION). The biodegradable and biocompatible properties of these magnetically responsive particles and capacity for rapid endocytosis into cells makes them a breakthrough in targeted therapy. This review further discusses specific applications of magnetic targeting approaches including myocardial regeneration, endothelization of implantable cardiovascular devices and other regenerative medicine applications.