Methods and systems (10, 54, 72) are provided for administering phototherapy to an injured tissue in a living subject by delivering visible or infrared biostimulatory energy to bone marrow at a dose sufficient to cause mesenchymal stem cells to appear in the injured tissue. The energy may be coherent light and can be administered transcutaneously, subcutaneously, or via an intramedullary probe (74). The technique is useful for treating many types of tissue injury, including ischemic cardiac and renal conditions.