Stem cell therapy efficiently targets the brain for most neurological disorders like migraine, Parkinsonism, schizophrenia, Alzheimer’s disease, and brain injury. The major obstacles in potential brain targeting are the physiological barriers like blood-brain-barrier and bloodcerebrospinal fluid barrier. The conventional injectable route or direct transplantation of stem cells results in brain injury and is less feasible clinically. The alternative to these invasive routes is the intranasal route that is non-invasive, easily repeatable technique and highly effective in brain targeting without crossing the blood-brain barrier. Extensive research has been undertaken for the delivery of stem cells to the brain via the intranasal route that holds great potential in overcoming the existing barriers. Nanotechnology is emerging as a novel interdisciplinary field in the arena of stem cell research. The combination of nanotechnology coupled with stem cell therapy has led to synergistic outcomes in diagnostic and therapeutic applications of neurological diseases. This review provides insights into stem cell-based nanotherapy for brain targeting via the intranasal route.