Infections caused by drug-resistant pathogens are rapidly increasing in incidence and pose an urgent global health concern. New treatments are needed to address this critical situation while preventing further resistance acquired by the pathogens. One promising approach is antimicrobial photodynamic therapy (PDT), a technique that selectively damages pathogenic cells through reactive oxygen species (ROS) that have been deliberately produced by light-activated chemical reactions via a photosensitiser. There are currently some limitations to its wider deployment, including aggregation, hydrophobicity, and sub-optimal penetration capabilities of the photosensitiser, all of which decrease the production of ROS and lead to reduced therapeutic performance. In combination with nanoparticles, however, these challenges may be overcome. Their small size, functionalisable structure, and large contact surface allow a high degree of internalization by cellular membranes and tissue barriers. In this review, we first summarise the mechanism of PDT action and the interaction between nanoparticles and the cell membrane. We then introduce the categorisation of nanoparticles in PDT, acting as nanocarriers, photosensitising molecules, and transducers, in which we highlight their use against a range of bacterial and fungal pathogens. We also compare the antimicrobial efficiency of nanoparticles to unbound photosensitisers and examine the relevant safety considerations. Finally, we discuss the use of nanoparticulate drug delivery systems in clinical applications of antimicrobial PDT.