With the rapid development of stem cell therapy, it has been increasingly important to understand the cell fate (eg., location, migration, interaction, and differentiation) of transplanted cells in a living body. Feasible and effective labeling strategies with advanced labeling agents are the key factors to realize long-term tracking of the cells. In this study, we investigated the migration and localization of bone marrow stromal cells (BMSCs) in an ischemic stroke model using organic dots with aggregation-induced emission (AIE dots) as the fluorescent tracker. The cell penetrating peptide functionalized AIE dots show far-red/near-infrared (FR/NIR) emission with excellent internalization efficiency and low cytotoxicity to BMSCs. The AIE dots have shown much better performance in long-term BMSC tracing in vitro, using commercial Qtracker 655 as the benchmark. Upon transplantation into an ischemic stroke rat, the BMSCs labeled with AIE dots could preferentially migrate to the injured brain tissue after 7 days. As a result, the very first study using biocompatible AIE dots for therapeutic cell tracking highlights their great potential in fundamental research during stem cell transplantation, which will benefit the overall outcome of cell-based therapy.