Stem cells (SCs) are cells with strong proliferation ability, multilineage differentiation potential and self-renewal capacity. SC transplantation represents an important therapeutic advancement for the treatment strategy of neurological diseases, both in the preclinical experimental and clinical settings. Innovative and breakthrough SC labelling and tracking technologies are widely used to monitor the distribution and viability of transplanted cells non-invasively and longitudinally. Here we summarised the research progress of the main tracers, labelling methods and imaging technologies involved in current SC tracking technologies for various neurological diseases. Finally, the applications, challenges and unresolved problems of current SC tracing technologies were discussed.