Biofilm-associated infections pose a huge burden on healthcare systems worldwide, with recurrent lung infections occurring due to the persistence of biofilm bacteria populations. In cystic fibrosis (CF), thick viscous mucus acts not only as a physical barrier, but also serves as a nidus for infection. Increased antibiotic resistance in the recent years indicates that current therapeutic strategies aimed at biofilm-associated infections are “failing”, emphasizing the need to develop new and improved drug delivery systems with higher efficacy and efficiency. Magnetic nanoparticles (MNPs) have unique and favourable properties encompassing biocompatibility, biodegradability, magnetic and heat-mediated characteristics, making them suitable drug carriers. Additionally, an external magnetic force can be applied to enhance drug delivery to target sites, acting as “nano-knives”, cutting through the bacterial biofilm layer and characteristically thick mucus in CF. In this review, we explore the multidisciplinary approach of using current and novel MNPs as vehicles of drug delivery. Although many of these offer exciting prospects for future biofilm therapeutics, there are also major challenges of this emerging field that need to be addressed.