Brain diseases, including tumors and neurodegenerative disorders, are among the most serious health problems. Non-invasively high-resolution imaging methods are required to gain anatomical structures and information of the brain. In addition, efficient diagnosis technology is also needed to treat brain disease. Rare-earth based materials possess unique optical properties, superior magnetism, and high X-ray absorption abilities, enabling high-resolution imaging of the brain through magnetic resonance imaging, computed tomography imaging, and fluorescence imaging technologies. In addition, rare-earth based materials can be used to detect, treat, and regulate of brain diseases through fine modulation of their structures and functions. Importantly, rare-earth based materials coupled with biomolecules such as antibodies, peptides, and drugs can overcome the blood-brain barrier and be used for targeted treatment. Herein, this review highlights the rational design and application of rare-earth based materials in brain imaging, therapy, monitoring, and neuromodulation. Furthermore, the development prospect of rare-earth based materials is briefly introduced.