Methods of enhancing stem cell therapy through the administration of low level light energy are provided in several embodiments. Some embodiments comprise irradiating stem cells before or after implantation at a target tissue having loss of function due to damage or disease, with a resultant increase in the efficacy of the cell therapy. In some embodiments, light energy enhances one or more of the viability, proliferation, migration or engraftment of the stem cells, thereby enhancing the therapeutic effects of the irradiated cells during cell therapy.