T lymphocytes play a central role in many human immunologic disorders including autoimmune and alloimmune diseases. In hematopoietic stem cell transplant, acute graft-versus-host-disease (GVHD) is caused by an attack on the recipient’s tissues from donor allogeneic T cells. Selectively depleting GVHD-causing cells prior to transplant may prevent GVHD. In this report we have evaluated 24 chalcogenorhodamine photosensitizers for their ability to selectively deplete reactive T lymphocytes, and identified the photosensitizer 2-Se-Cl that accumulates in stimulated T cells in proportion to oxidative phosphorylation (OXPHOS). The photosensitizer is also a potent stimulator of P-glycoprotein (P-pg). Enhanced P-gp activity promotes the efficient removal of photosensitizer not sequestered in mitochondria, and protects resting lymphocytes essential for antipathogen and antitumor responses. To evaluate the selective depletion of alloimmune responses, donor C57BL/6 splenocytes were cocultured for 5 days with irradiated Balb/c splenocytes, and then photodepleted (PD). PD-treated splenocytes were then infused into lethally irradiated BALB/c (same-party) or C3H/HeJ (third-party) mice. Same-party mice that received PD-treated splenocytes at the time of transplant lived 100 days without evidence of GVHD. In contrast, all mice that received untreated primed splenocytes and third-party mice that received PD-treated splenocytes died of lethal GVHD. To evaluate the preservation of antiviral immune responses, acute lymphocytic choriomeningitis virus (LCMV) infection was employed. After PD, expansion of antigen-specific naïve CD8+ T cells and viral clearance remained fully intact. The high selectivity of this novel photosensitizer may have broad applications and provide alternative treatment options for patients with T lymphocyte mediated diseases.