Brain diseases are characterized by high incidence, disability, and mortality rates. Their elusive nature poses a significant challenge for early diagnosis. Magnetic particle imaging (MPI) is a novel imaging technique with high sensitivity, high temporal resolution, and no ionizing radiation. It relies on the nonlinear magnetization response of superparamagnetic iron oxide nanoparticles (SPIONs), allowing visualization of the spatial concentration distribution of SPIONs in biological tissues. MPI is expected to become a mainstream technology for the early diagnosis of brain diseases, such as cancerous, cerebrovascular, neurodegenerative, and inflammatory diseases. This review provides an overview of the principles of MPI, explores its potential applications in brain diseases, and discusses the prospects for the diagnosis and management of these diseases.