Earlier chapters in this book describe the synthesis and characterisation of magnetic nanoparticles, their biofunctionalisation and the medical applications they enable. This chapter focuses on magnet systems design and control: how should magnets be designed, where should they be placed and when should they be turned on and off so as to begin to understand how to better direct magnetic nanoparticles to in vivo targets? Shaping of magnetic šelds and forces for directing therapy to disease locations is valuable for a wide range of clinical applications, and in this chapter, we will focus on just two: (1) magnetically pushing (injecting) nanoparticles to reach inner ear diseases and (2) development of methods for targeting deeper tissue tumours. Magnet design, optimisation and control will be informed by mathematical modelling of magnetic šelds, forces and the resulting in vivo particle transport.