Stem cell research is a field that has attracted tremendous attention in recent years. How to precisely label and track stem cells after administration is important not only for fundamental stem cell research, but also for practical applications of stem cell technology in the clinic. Various stem cell labeling and tracking strategies, many of which utilize nanotechnology, have been reported by many different groups. Here, recent progress in the development of various functional nanomaterials for stem cell labeling and tracking is reviewed and the current challenges and future prospects are discussed.