Post-transplantation cyclophosphamide (PTCy) reduces the risks of severe acute and chronic graft-versus-host disease (GVHD) after allogeneic hematopoietic cell transplantation (HCT). Yet, the standard clinical dose and timing of PTCy were partly extrapolated from MHC-matched skin allografting models and were partly empirical. Here we investigated the impact of differential dosing and timing of PTCy on its efficacy in preventing GVHD in a murine MHC-haploidentical HCT model. Administration of PTCy on days +3/+4 was superior to administration on days +1/+2, +5/+6, or +7/+8, whereas low-dose (10 mg/kg/day) PTCy on days +1/+2 actually led to accelerated death. Although the optimal timing of PTCy dosing was day +2 or +3 in the skin allografting models, in our MHC-haploidentical HCT model, PTCy on days +2/+3 was inferior to PTCy on days +3/+4 at lower doses. PTCy administered on days +3/+4, +4/+5, or +3/+5 were similarly efficacious. Single-day versus 2-day dosing schedules demonstrated that PTCy is maximally effective when given on day +4. Flow cytometric analysis showed that optimal PTCy dosing schedules both decreased alloreactive CD4⁺CD25⁻Foxp3⁻ T cell proliferation at day +7 and allowed preferential CD4⁺CD25⁺Foxp3⁺ T cell reconstitution at day +21, suggesting that this combination may be a potential predictive biomarker of successful GVHD prevention by PTCy. These results show that the dose, timing, and cumulative exposure of PTCy all are critical for its efficacy in preventing GVHD. We are currently investigating the clinical relevance of these findings in a protocol seeking to optimize PTCy dose and timing and test these T cell endpoints as candidate biomarkers of successful GVHD prevention by PTCy.