This study was aimed to investigate the effect of PTD-mFoxp3 fusion protein on graft-versus-host disease (GVHD) after allogeneic bone marrow transplantation. The 10-weeks-old C57BL/6 mice as recipients were randomly divided into three groups (A,B and C), 10 mice were in each group. The mice on day of transplantation as on day 0 received total body irradiation (TBI) 6.0 Gy, then the bone marrow cells (BMC) from BALB/c mice were injected through tail vein within 4-6 hours. At 2 days before transplantation and 0, 1, 3, 5, 7, 9 and 13 days after transplantation, mice in group A were injected with saline, mice in group B were injected with mFoxp3 protein and mice in group C were injected with PTD-mFoxp3 fusion protein. Symptoms of GVHD, survival time and histopathological changes were observed. The establishment of mixed chimerism was determined by flow cytometry in day 60, and IL-2 and IFN-γ expression profiles in the recipient peripheral blood were assessed by ELISA. The results showed that the mean survival time of recipients in group A,B and C was (32.95 ± 5.48) , (38.00 ± 5.45) and (55.30 ± 3.15) respectively. Graft rejection was observed in the liver and small intestine specimens of group A and group B. The serum levels of IL-2 and IFN-γ significantly decreased in the recipients of group C, as compared with the other groups. The flow cytometry analysis revealed that the survival recipient mice developed high chimerism levels, the percentages of donor cells in group A,B and C were (79.46 ± 1.80) %, (79.13 ± 2.23) % and (85.92 ± 2.82) % respectively. It is concluded that PTD-mFoxp3 fusion protein can reduce the incidence and mortality of GVHD after allogeneic bone marrow transplantation.