Manganese-enhanced magnetic resonance imaging (MEMRI) relies on the strong paramagnetism of Mn 2+. Mn 2+ is a calcium ion analog and can enter excitable cells through voltage-gated calcium channels. Mn 2+ can be transported along the axons of neurons via microtubule-based fast axonal transport. Based on these properties, MEMRI is used to describe neuroanatomical structures, monitor neural activity, and evaluate axonal transport rates. The application of MEMRI in preclinical animal models of central nervous system (CNS) diseases can provide more information for the study of disease mechanisms. In this article, we provide a brief review of MEMRI use in CNS diseases ranging from neurodegenerative diseases to brain injury and spinal cord injury.