Neurodegenerative and muscle diseases bear both complex and multifactorial pathologies. An efficacious and robust therapeutic option to treat these diseases is yet to be elucidated. At such a time, mesenchymal stem cells have drawn significant attention due to their immunomodulatory and regenerative properties. Accumulating evidence has proposed the capability of MSCs to serve multiple roles in a broad spectrum of diseases by secretion of trophic or paracrine factors. In the present review, we will look into the recent literature and discuss the therapeutic functions of MSCs and their potential to treat various neurodegenerative (Alzheimer's, Parkinson's, and Huntington's disease) and muscle (Duchenne muscular dystrophy, myopathy, and multiple sclerosis) diseases.