Carbon nanotubes and nanofibers are intriguing materials for medical applications due to their unique mechanical, electrical, and surface properties which have been shown to enhance in vitro neural cell functions compared to other central nervous system implant materials such as silicon. The objective of this in vivo study was to determine if stem cells can be combined with carbon nanofibers in the treatment of stroke damaged neural tissue in rats. Both hydrophobic and hydrophilic carbon nanofibers were mixed with stem cells and implanted into stroke damaged brains of rats for up to 3 weeks. Results | demonstrated the ability of stem cells to differentiate into neurons when injected with either, hydrophobic or hydrophilic carbon nanofibers into stroke damaged neural tissue. Hydrophobic nanofibers increased stem cell differentiation more than hydrophilic carbon nanofibers. Moreover, little scar tissue formation was observed surrounding both types of carbon nanofibers when implanted into the brain. Such results indicate promise for the use of carbon nanofibers as novel stem cell delivery vehicles for treating stroke damaged neural tissue.