Stem cell-based therapies have emerged as promising platforms with the potential to treat serious diseases that are incurable by traditional medical approaches. To optimize the overall outcomes, it is important to understand the fate of transplanted stem cells (e.g., localization, migration, engraftment, survival, proliferation and differentiation). Fluorescent nanoparticles with good photostability and minimal perturbation of cell functions hold great promise for distinguishing transplanted stem cells from host tissues with high resolution, showing advantages over traditional histological methods. This review aims to summarize the recent advances in the use of fluorescent nanoparticles for the direct labelling of stem cells and the applications of such nanoparticles in stem cell tracking. The relevant fluorescent nanoparticles, including quantum dots, organic fluorogen-doped nanoparticles, fluorescent nanodiamonds, and upconversion nanoparticles are discussed. The advantages and limitations of the currently available fluorescent trackers are summarized, and perspectives on new research opportunities are discussed.