Plerixafor, a hematopoietic stem cell mobilization agent, increases the peripheral blood content of effector and regulatory T cells and may have beneficial effects on cardiac allograft vasculopathy. The aim of the current study was to evaluate its effects in a murine aortic allograft model using different application procedures. Allogeneic donor aorta grafts (n = 8/group) from C57BL/6 mice(H2b) were abdominally transplanted into CBA mice (H2k). Plerixafor application was performed either continuously for 14 d using abdominally implanted osmotic pumps (1 mg/kg/d) or i.p. with a single dose (1 and 5 mg/kg) on day 0 or pulsed injections of 1 mg/kg on days 0, 7, 14, and 21. Cell distribution was monitored by FACS. Aortic grafts were evaluated for neointima development by Elastica-van-Gieson on day 30. Immunofluorescence and intragraft gene expression analysis were performed. On day 14, significantly fewer hematopoietic stem cells were found in the bone marrow of all plerixafor-treated mice. In the pulsed application group, significantly more hematopoietic stem cells were found in the peripheral blood on day 14 (0.045 ± 0.002%; p < 0.01 [pulsed]; versus 0.0068 ± 0.002% [control]) and also more regulatory T cells. PCR revealed lower inflammatory cytokines. The luminal occlusion was significantly reduced in the pulsed treated group (33.65 ± 8.84 versus 53.13 ± 12.41) going along with decreased neointimal CD4+ T cell and plasmacytoid dendritic cell infiltration, as well as less smooth muscle cell proliferation. The application of plerixafor attenuates chronic rejection in aortic allografts via immunomodulatory effects. Injection of repeated low-dose plerixafor is the most effective application form in the aortic transplant model.