This study aimed to evaluate the impact of standard-dose dipeptidyl peptidase-4 inhibitors (DPP-4i) on the incidence of graft-versus-host disease (GVHD) after allogeneic hematopoietic cell transplantation (HCT). We retrospectively evaluated 207 diabetes mellitus patients undergoing allogeneic HCT between 2010 and 2019. The 100-day cumulative incidences (CI) of grade II–IV acute GVHD (aGVHD) in patients who took DPP-4i from day − 1 to 14, those who did not, and those who discontinued DPP-4i within 10 days after HCT because of difficulty taking the medicine were 33.9%, 32.8%, and 60.0% (P = 0.063), respectively. With regard to chronic GVHD (cGVHD), taking DPP-4i between days 21 and 60 was associated with a trend toward lower incidence of cGVHD (1-year CI: 25.4% vs. 35.6%, P = 0.094). In a multivariate analysis, the administration of DPP-4i between days 21 and 60 was significantly associated with lower incidence of cGVHD (hazard ratio 0.53, 95% confidence interval 0.30–0.96, P = 0.035). It was difficult to interpret the impact of standard-dose DPP-4i on the development of aGVHD since an inability to continue oral medication was significantly associated with higher incidence of aGVHD. On the other hand, taking DPP-4i over days 21–60 may suppress the development of cGVHD.