It is well recognized that neuroinflammation is involved in the pathogenesis of various neurodegenerative diseases. Microglia and astrocytes are major pathogenic components within this process and known to respond to proinflammatory mediators released from immune cells such as mast cells. Mast cells reside in the brain and are an important source of inflammatory molecules. Mast cell interactions with glial cells and neurons result in the release of mediators such as cytokines, proteases and reactive oxygen species. During neuroinflammation, excessive levels of these mediators can influence neurogenesis, neurodegeneration and blood-brain barrier (BBB) permeability. Mast cells are considered first responders and are able to initiate and magnify immune responses in the brain. Their possible role in neurodegenerative disorders such as multiple sclerosis, Alzheimer’s disease and autism has gained increasing interest. We discuss the possible involvement of mast cells and their mediators in neurogenesis, neurodegeneration and BBB permeability and their role in neuronal disorders such as cerebral ischemia, traumatic brain injury, neuropathic pain, multiple sclerosis, Alzheimer’s disease, migraine, autism, and depression.