Exosomes are nano-vesicles secreted by different cell types, which enable intercellular communication of cells in their vicinity or at distant sites. Recent studies established that exosomes derived from mesenchymal stem cells (MSC-exo) carry miRNA and proteins that can promote regeneration and immunomodulation processes in damaged tissues. We developed a method for longitudinal and quantitative in vivo neuroimaging of exosomes, based on the superior visualization abilities of classical X-ray computed tomography (CT), and combined with gold nanoparticles (GNPs) as labeling agents. Using this technique, we tracked the migration and homing patterns of MSC-exo in different and common brain pathologies in mice, after intranasal delivery. Moreover, in BTBR mice, which are an accepted model of evaluating autistic-like behaviors. We found that intranasal administration of MSC-exo social interaction and reduced repetitive behaviors. Moreover, the treatment led to increases male to female ultrasonic vocalizations and significant improvement in maternal behaviors of pup retrieval. The marked beneficial effects of the exosomes in mice models may translate to a novel, non-invasive, and therapeutic strategy to reduce the symptoms in autism spectrum disorders.