Exosomes are lipid bilayer vesicles released by cells and serve as natural carriers for cell–cell communication. Exosomes provide a promising approach to the diagnosis and treatment of diseases and are considered as an alternative to cell therapy. However, one main restriction in their clinical application is that the current understanding of these vesicles, especially their in vivo behaviors and distributions, remains inadequate. Here, we reviewed the current and emerging methods for in vivo imaging and tracking of exosomes, including fluorescence imaging, bioluminescence imaging, nuclear imaging, X-ray imaging, magnetic resonance imaging, photoacoustic imaging, and multimodal imaging. In vivo imaging and tracking of exosomes by these methods can help researchers further understand their uptake mechanism, biodistribution, migration, function, and therapeutic performance. The pioneering studies in this field can elucidate many unknown exosomal behaviors at different levels. We discussed the advantages and limitations of each labeling and imaging strategy. The advances in labeling and in vivo imaging will expand our understanding of exosomes and promote their clinical application. We finally provide a perspective and discuss several important issues that need to be explored in future research. This review highlights the values of efficient, sensitive, and biocompatible exosome labeling and imaging techniques in disease theranostics.